Differential abundance

This function returns the fold change and associated p value for a differential abundance analysis. It is useful for finding taxa with an abundance that strongly differs between two groups of samples, such as finding taxa with abundance that differs between skin and saliva samples. This function allows one to recreate the results of differential abundance analysis from MicrobiomeDB.org. However, we recognize that this function makes some assumptions about the data which may not be valid in other contexts. For better support of longitudinal studies or metabolomic data, for example, please see our wrapper/ helper methods for Maaslin2 (MicrobiomeDB::Maaslin2) and DESeq2 (DESeqDataSetFromCollection).

Usage

differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

# S4 method for CollectionWithMetadata,character,missingOrNULL,missingOrNULL
differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

# S4 method for CollectionWithMetadata,character,function,missingOrNULL
differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

# S4 method for CollectionWithMetadata,character,character,missingOrNULL
differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

# S4 method for CollectionWithMetadata,character,function,function
differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

# S4 method for CollectionWithMetadata,character,character,character
differentialAbundance(
  data,
  covariate,
  groupA,
  groupB,
  method = c("Maaslin2", "DESeq2"),
  verbose = c(TRUE, FALSE)
)

Arguments

data

AbundanceData object

covariate

character vector giving the name of a metadata variable of interest. If this variable has only two values, you do not need to provide functions for arguments groupA and groupB.

groupA

A function that takes a vector of values and returns TRUE or FALSE for each value. This will be used to assign samples to groupA. In the specific case of covariate being a categorical variable, this can be a character vector of values to be included in groupA.

groupB

A function that takes a vector of values and returns TRUE or FALSE for each value. This will be used to assign samples to groupB. If not provided, groupB will be the complement of groupA. In the specific case of covariate being a categorical variable, this can be a character vector of values to be included in groupB.

method

string defining the the differential abundance method. Accepted values are 'DESeq2' and 'Maaslin2'. Default is 'Maaslin2', as 'DESeq2' only supports counts.

verbose

boolean indicating if timed logging is desired

Value

ComputeResult object

Examples

## a continuous variable
diffAbundOutput <- MicrobiomeDB::differentialAbundance(
       getCollection(
         microbiomeData::DiabImmune, 
  '16S (V4) Genus (Relative taxonomic abundance analysis)'), 
       "breastfed_duration", 
       groupA = function(x) {x<300},
       groupB = function(x) {x>=300},
       method='Maaslin2', 
       verbose=TRUE
)
#> 
#> 2024-06-26 14:27:58.969626 Found NAs in specified variable. Removing these records.
#> 
#> 2024-06-26 14:27:59.04826 Received abundance table with 2533 samples and 674 taxa.
#> 
#> 2024-06-26 14:27:59.050119 Found 2533 samples with a value for breastfed_duration in either groupA or groupB. The calculation will continue with only these samples.
#> [1] "Creating output folder"
#> [1] "Creating output feature tables folder"
#> [1] "Creating output fits folder"
#> 2024-06-26 14:27:59.125741 INFO::Writing function arguments to log file
#> 2024-06-26 14:27:59.129536 INFO::Verifying options selected are valid
#> 2024-06-26 14:27:59.130041 INFO::Determining format of input files
#> 2024-06-26 14:27:59.131446 INFO::Input format is data samples as rows and metadata samples as rows
#> 2024-06-26 14:27:59.152843 INFO::Formula for fixed effects: expr ~  breastfed_duration
#> 2024-06-26 14:27:59.153692 INFO::Filter data based on min abundance and min prevalence
#> 2024-06-26 14:27:59.154171 INFO::Total samples in data: 2533
#> 2024-06-26 14:27:59.154629 INFO::Min samples required with min abundance for a feature not to be filtered: 253.300000
#> 2024-06-26 14:27:59.171082 INFO::Total filtered features: 522
#> 2024-06-26 14:27:59.172034 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Candidatus.Arthromitus, Candidatus.Obscuribacter, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Faecalicoccus, Faecalitalea, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavobacterium, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Marvinbryantia, Massilia, Megamonas, Merdibacter, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Myxococcus, NK4A214.group, Nakamurella, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phaseolibacter, Phocea, Phyllobacterium, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Propionimicrobium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudoflavonifractor, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tetragenococcus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis..EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_., unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_., unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97
#> 2024-06-26 14:27:59.178537 INFO::Total filtered features with variance filtering: 0
#> 2024-06-26 14:27:59.179066 INFO::Filtered feature names from variance filtering:
#> 2024-06-26 14:27:59.17954 INFO::Running selected normalization method: TSS
#> 2024-06-26 14:27:59.227182 INFO::Applying z-score to standardize continuous metadata
#> 2024-06-26 14:27:59.230086 INFO::Running selected transform method: LOG
#> 2024-06-26 14:27:59.287842 INFO::Running selected analysis method: LM
#> 2024-06-26 14:27:59.288555 INFO::Fitting model to feature number 1, Actinomyces
#> 2024-06-26 14:27:59.292876 INFO::Fitting model to feature number 2, Agathobacter
#> 2024-06-26 14:27:59.29678 INFO::Fitting model to feature number 3, Akkermansia
#> 2024-06-26 14:27:59.300677 INFO::Fitting model to feature number 4, Alistipes
#> 2024-06-26 14:27:59.304555 INFO::Fitting model to feature number 5, Anaerostipes
#> 2024-06-26 14:27:59.308449 INFO::Fitting model to feature number 6, Atopobium
#> 2024-06-26 14:27:59.31231 INFO::Fitting model to feature number 7, Bacteroides
#> 2024-06-26 14:27:59.316167 INFO::Fitting model to feature number 8, Barnesiella
#> 2024-06-26 14:27:59.32003 INFO::Fitting model to feature number 9, Bifidobacterium
#> 2024-06-26 14:27:59.323894 INFO::Fitting model to feature number 10, Bilophila
#> 2024-06-26 14:27:59.327753 INFO::Fitting model to feature number 11, Blautia
#> 2024-06-26 14:27:59.331641 INFO::Fitting model to feature number 12, Butyricicoccus
#> 2024-06-26 14:27:59.335506 INFO::Fitting model to feature number 13, CAG.352
#> 2024-06-26 14:27:59.339349 INFO::Fitting model to feature number 14, Campylobacter
#> 2024-06-26 14:27:59.343196 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group
#> 2024-06-26 14:27:59.347039 INFO::Fitting model to feature number 16, Clostridioides
#> 2024-06-26 14:27:59.35088 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1
#> 2024-06-26 14:27:59.354735 INFO::Fitting model to feature number 18, Colidextribacter
#> 2024-06-26 14:27:59.358609 INFO::Fitting model to feature number 19, Collinsella
#> 2024-06-26 14:27:59.362461 INFO::Fitting model to feature number 20, Coprobacillus
#> 2024-06-26 14:27:59.366328 INFO::Fitting model to feature number 21, Coprococcus
#> 2024-06-26 14:27:59.370202 INFO::Fitting model to feature number 22, DTU089
#> 2024-06-26 14:27:59.374062 INFO::Fitting model to feature number 23, Dialister
#> 2024-06-26 14:27:59.377908 INFO::Fitting model to feature number 24, Dorea
#> 2024-06-26 14:27:59.381795 INFO::Fitting model to feature number 25, Eggerthella
#> 2024-06-26 14:27:59.385638 INFO::Fitting model to feature number 26, Eisenbergiella
#> 2024-06-26 14:27:59.389505 INFO::Fitting model to feature number 27, Enterococcus
#> 2024-06-26 14:27:59.393379 INFO::Fitting model to feature number 28, Erysipelatoclostridium
#> 2024-06-26 14:27:59.397272 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003
#> 2024-06-26 14:27:59.401197 INFO::Fitting model to feature number 30, Escherichia.Shigella
#> 2024-06-26 14:27:59.405088 INFO::Fitting model to feature number 31, Faecalibacterium
#> 2024-06-26 14:27:59.408945 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group
#> 2024-06-26 14:27:59.412839 INFO::Fitting model to feature number 33, Flavonifractor
#> 2024-06-26 14:27:59.416724 INFO::Fitting model to feature number 34, Fusicatenibacter
#> 2024-06-26 14:27:59.42064 INFO::Fitting model to feature number 35, Fusobacterium
#> 2024-06-26 14:27:59.424487 INFO::Fitting model to feature number 36, Gemella
#> 2024-06-26 14:27:59.428369 INFO::Fitting model to feature number 37, Granulicatella
#> 2024-06-26 14:27:59.432291 INFO::Fitting model to feature number 38, Haemophilus
#> 2024-06-26 14:27:59.436173 INFO::Fitting model to feature number 39, Holdemania
#> 2024-06-26 14:27:59.44 INFO::Fitting model to feature number 40, Hungatella
#> 2024-06-26 14:27:59.443821 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.
#> 2024-06-26 14:27:59.447726 INFO::Fitting model to feature number 42, Intestinibacter
#> 2024-06-26 14:27:59.45159 INFO::Fitting model to feature number 43, Intestinimonas
#> 2024-06-26 14:27:59.455418 INFO::Fitting model to feature number 44, Klebsiella
#> 2024-06-26 14:27:59.459308 INFO::Fitting model to feature number 45, Lachnoclostridium
#> 2024-06-26 14:27:59.463194 INFO::Fitting model to feature number 46, Lachnospira
#> 2024-06-26 14:27:59.467076 INFO::Fitting model to feature number 47, Lachnospiraceae.ND3007.group
#> 2024-06-26 14:27:59.470941 INFO::Fitting model to feature number 48, Lachnospiraceae.NK4A136.group
#> 2024-06-26 14:27:59.474793 INFO::Fitting model to feature number 49, Lachnospiraceae.UCG.001
#> 2024-06-26 14:27:59.478694 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.004
#> 2024-06-26 14:27:59.482572 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.009
#> 2024-06-26 14:27:59.486465 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.010
#> 2024-06-26 14:27:59.490336 INFO::Fitting model to feature number 53, Lactobacillus
#> 2024-06-26 14:27:59.494218 INFO::Fitting model to feature number 54, Lactococcus
#> 2024-06-26 14:27:59.498143 INFO::Fitting model to feature number 55, Mannheimia
#> 2024-06-26 14:27:59.502059 INFO::Fitting model to feature number 56, Megasphaera
#> 2024-06-26 14:27:59.505928 INFO::Fitting model to feature number 57, Monoglobus
#> 2024-06-26 14:27:59.509805 INFO::Fitting model to feature number 58, Neisseria
#> 2024-06-26 14:27:59.513662 INFO::Fitting model to feature number 59, Odoribacter
#> 2024-06-26 14:27:59.517482 INFO::Fitting model to feature number 60, Oscillibacter
#> 2024-06-26 14:27:59.521439 INFO::Fitting model to feature number 61, Oscillospira
#> 2024-06-26 14:27:59.525321 INFO::Fitting model to feature number 62, Parabacteroides
#> 2024-06-26 14:27:59.529197 INFO::Fitting model to feature number 63, Parasutterella
#> 2024-06-26 14:27:59.543642 INFO::Fitting model to feature number 64, Phascolarctobacterium
#> 2024-06-26 14:27:59.548198 INFO::Fitting model to feature number 65, Prevotella
#> 2024-06-26 14:27:59.552128 INFO::Fitting model to feature number 66, Pseudomonas
#> 2024-06-26 14:27:59.556007 INFO::Fitting model to feature number 67, Romboutsia
#> 2024-06-26 14:27:59.559973 INFO::Fitting model to feature number 68, Roseburia
#> 2024-06-26 14:27:59.563867 INFO::Fitting model to feature number 69, Rothia
#> 2024-06-26 14:27:59.567776 INFO::Fitting model to feature number 70, Ruminococcus
#> 2024-06-26 14:27:59.571711 INFO::Fitting model to feature number 71, Sellimonas
#> 2024-06-26 14:27:59.575631 INFO::Fitting model to feature number 72, Solobacterium
#> 2024-06-26 14:27:59.579544 INFO::Fitting model to feature number 73, Staphylococcus
#> 2024-06-26 14:27:59.58345 INFO::Fitting model to feature number 74, Streptococcus
#> 2024-06-26 14:27:59.587354 INFO::Fitting model to feature number 75, Subdoligranulum
#> 2024-06-26 14:27:59.591286 INFO::Fitting model to feature number 76, Sutterella
#> 2024-06-26 14:27:59.595195 INFO::Fitting model to feature number 77, Terrisporobacter
#> 2024-06-26 14:27:59.599063 INFO::Fitting model to feature number 78, Turicibacter
#> 2024-06-26 14:27:59.603004 INFO::Fitting model to feature number 79, Tuzzerella
#> 2024-06-26 14:27:59.606886 INFO::Fitting model to feature number 80, Tyzzerella
#> 2024-06-26 14:27:59.61076 INFO::Fitting model to feature number 81, UBA1819
#> 2024-06-26 14:27:59.614646 INFO::Fitting model to feature number 82, UCG.002
#> 2024-06-26 14:27:59.618523 INFO::Fitting model to feature number 83, UCG.003
#> 2024-06-26 14:27:59.622417 INFO::Fitting model to feature number 84, UCG.005
#> 2024-06-26 14:27:59.626306 INFO::Fitting model to feature number 85, Veillonella
#> 2024-06-26 14:27:59.630218 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group
#> 2024-06-26 14:27:59.634091 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group
#> 2024-06-26 14:27:59.637968 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group
#> 2024-06-26 14:27:59.64186 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group
#> 2024-06-26 14:27:59.645766 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group
#> 2024-06-26 14:27:59.649655 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group
#> 2024-06-26 14:27:59.653553 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group
#> 2024-06-26 14:27:59.657445 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group
#> 2024-06-26 14:27:59.661336 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group
#> 2024-06-26 14:27:59.665318 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group
#> 2024-06-26 14:27:59.669258 INFO::Fitting model to feature number 96, unclassified.Chloroplast
#> 2024-06-26 14:27:59.673131 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014
#> 2024-06-26 14:27:59.677037 INFO::Fitting model to feature number 98, unclassified.Clostridia
#> 2024-06-26 14:27:59.680943 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group
#> 2024-06-26 14:27:59.684824 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales
#> 2024-06-26 14:27:59.6887 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae
#> 2024-06-26 14:27:59.692623 INFO::Fitting model to feature number 102, unclassified.Mitochondria
#> 2024-06-26 14:27:59.696517 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae
#> 2024-06-26 14:27:59.70045 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus
#> 2024-06-26 14:27:59.704295 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales
#> 2024-06-26 14:27:59.708156 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae
#> 2024-06-26 14:27:59.71203 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group
#> 2024-06-26 14:27:59.72746 INFO::Counting total values for each feature
#> 2024-06-26 14:27:59.732669 INFO::Writing filtered data to file /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/features/filtered_data.tsv
#> 2024-06-26 14:27:59.907455 INFO::Writing filtered, normalized data to file /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/features/filtered_data_norm.tsv
#> 2024-06-26 14:28:00.086099 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/features/filtered_data_norm_transformed.tsv
#> 2024-06-26 14:28:00.371469 INFO::Writing residuals to file /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/fits/residuals.rds
#> 2024-06-26 14:28:00.426293 INFO::Writing fitted values to file /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/fits/fitted.rds
#> 2024-06-26 14:28:00.445253 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/all_results.tsv
#> 2024-06-26 14:28:00.446947 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d631b44f2e/significant_results.tsv
#> 
#> 2024-06-26 14:28:00.448813 Completed method=Maaslin2. Formatting results.
#> 
#> 2024-06-26 14:28:00.45197 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration , method =  Maaslin2 , groupA = groupA , groupB =  groupB

## same variable, using DESeq2
diffAbundOutput <- MicrobiomeDB::differentialAbundance(
       getCollection(
             microbiomeData::DiabImmune, 
             '16S (V4) Genus (Absolute taxonomic abundance analysis)'), 
       "breastfed_duration", 
       groupA = function(x) {x<300},
       groupB = function(x) {x>=300},
       method='DESeq2', 
       verbose=TRUE
)
#> 
#> 2024-06-26 14:28:00.499566 Integer values detected. Converting collection to AbsoluteAbundanceData
#> 
#> 2024-06-26 14:28:00.646387 Found NAs in specified variable. Removing these records.
#> 
#> 2024-06-26 14:28:00.776598 Received abundance table with 2533 samples and 674 taxa.
#> 
#> 2024-06-26 14:28:00.778358 Found 2533 samples with a value for breastfed_duration in either groupA or groupB. The calculation will continue with only these samples.
#> converting counts to integer mode
#> Warning: some variables in design formula are characters, converting to factors
#> using pre-existing size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> -- replacing outliers and refitting for 267 genes
#> -- DESeq argument 'minReplicatesForReplace' = 7 
#> -- original counts are preserved in counts(dds)
#> estimating dispersions
#> fitting model and testing
#> 
#> 2024-06-26 14:28:40.350097 Completed method=DESeq2. Formatting results.
#> 
#> 2024-06-26 14:28:40.353057 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration , method =  DESeq2 , groupA = groupA , groupB =  groupB

## a categorical variable with 3 values, one of which we exclude
diffAbundOutput <- MicrobiomeDB::differentialAbundance(
       getCollection(
  microbiomeData::DiabImmune, 
  '16S (V4) Genus (Relative taxonomic abundance analysis)'), 
       "country", 
       groupA = function(x) {x=="Russia"},
       groupB = function(x) {x=="Finland"},
       method='Maaslin2', 
       verbose=FALSE
)
#> [1] "Creating output folder"
#> [1] "Creating output feature tables folder"
#> [1] "Creating output fits folder"
#> 2024-06-26 14:28:40.641435 INFO::Writing function arguments to log file
#> 2024-06-26 14:28:40.645254 INFO::Verifying options selected are valid
#> 2024-06-26 14:28:40.645777 INFO::Determining format of input files
#> 2024-06-26 14:28:40.647226 INFO::Input format is data samples as rows and metadata samples as rows
#> 2024-06-26 14:28:40.660449 INFO::Formula for fixed effects: expr ~  country
#> 2024-06-26 14:28:40.661226 INFO::Filter data based on min abundance and min prevalence
#> 2024-06-26 14:28:40.661708 INFO::Total samples in data: 2692
#> 2024-06-26 14:28:40.66216 INFO::Min samples required with min abundance for a feature not to be filtered: 269.200000
#> 2024-06-26 14:28:40.690445 INFO::Total filtered features: 522
#> 2024-06-26 14:28:40.691664 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asticcacaulis, Aureimonas, Bacillus, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Marinilactibacillus, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylobacillus, Methylobacterium.Methylorubrum, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, Paenibacillus, Paeniclostridium, Paludicola, Papillibacter, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Piscinibacter, Planifilum, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Propionimicrobium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinivibrio, Sulfurospirillum, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis..EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_., unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gastranaerophilales, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_., unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97
#> 2024-06-26 14:28:40.698584 INFO::Total filtered features with variance filtering: 0
#> 2024-06-26 14:28:40.699138 INFO::Filtered feature names from variance filtering:
#> 2024-06-26 14:28:40.699603 INFO::Running selected normalization method: TSS
#> 2024-06-26 14:28:40.750641 INFO::Applying z-score to standardize continuous metadata
#> 2024-06-26 14:28:40.753641 INFO::Running selected transform method: LOG
#> 2024-06-26 14:28:40.815364 INFO::Running selected analysis method: LM
#> 2024-06-26 14:28:40.81609 INFO::Fitting model to feature number 1, Actinomyces
#> 2024-06-26 14:28:40.820568 INFO::Fitting model to feature number 2, Agathobacter
#> 2024-06-26 14:28:40.824667 INFO::Fitting model to feature number 3, Akkermansia
#> 2024-06-26 14:28:40.828682 INFO::Fitting model to feature number 4, Alistipes
#> 2024-06-26 14:28:40.832709 INFO::Fitting model to feature number 5, Anaerostipes
#> 2024-06-26 14:28:40.836707 INFO::Fitting model to feature number 6, Atopobium
#> 2024-06-26 14:28:40.840748 INFO::Fitting model to feature number 7, Bacteroides
#> 2024-06-26 14:28:40.844764 INFO::Fitting model to feature number 8, Barnesiella
#> 2024-06-26 14:28:40.848835 INFO::Fitting model to feature number 9, Bifidobacterium
#> 2024-06-26 14:28:40.852899 INFO::Fitting model to feature number 10, Bilophila
#> 2024-06-26 14:28:40.856937 INFO::Fitting model to feature number 11, Blautia
#> 2024-06-26 14:28:40.86091 INFO::Fitting model to feature number 12, Butyricicoccus
#> 2024-06-26 14:28:40.864928 INFO::Fitting model to feature number 13, CAG.352
#> 2024-06-26 14:28:40.868926 INFO::Fitting model to feature number 14, Campylobacter
#> 2024-06-26 14:28:40.872961 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group
#> 2024-06-26 14:28:40.876997 INFO::Fitting model to feature number 16, Clostridioides
#> 2024-06-26 14:28:40.881029 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1
#> 2024-06-26 14:28:40.885023 INFO::Fitting model to feature number 18, Colidextribacter
#> 2024-06-26 14:28:40.889045 INFO::Fitting model to feature number 19, Collinsella
#> 2024-06-26 14:28:40.893073 INFO::Fitting model to feature number 20, Coprobacillus
#> 2024-06-26 14:28:40.897099 INFO::Fitting model to feature number 21, Coprococcus
#> 2024-06-26 14:28:40.9011 INFO::Fitting model to feature number 22, Corynebacterium
#> 2024-06-26 14:28:40.90512 INFO::Fitting model to feature number 23, DTU089
#> 2024-06-26 14:28:40.909075 INFO::Fitting model to feature number 24, Dialister
#> 2024-06-26 14:28:40.913101 INFO::Fitting model to feature number 25, Dorea
#> 2024-06-26 14:28:40.9171 INFO::Fitting model to feature number 26, Eggerthella
#> 2024-06-26 14:28:40.921163 INFO::Fitting model to feature number 27, Eisenbergiella
#> 2024-06-26 14:28:40.925151 INFO::Fitting model to feature number 28, Enterococcus
#> 2024-06-26 14:28:40.929186 INFO::Fitting model to feature number 29, Erysipelatoclostridium
#> 2024-06-26 14:28:40.933181 INFO::Fitting model to feature number 30, Erysipelotrichaceae.UCG.003
#> 2024-06-26 14:28:40.937225 INFO::Fitting model to feature number 31, Escherichia.Shigella
#> 2024-06-26 14:28:40.941269 INFO::Fitting model to feature number 32, Faecalibacterium
#> 2024-06-26 14:28:40.945282 INFO::Fitting model to feature number 33, Family.XIII.AD3011.group
#> 2024-06-26 14:28:40.949271 INFO::Fitting model to feature number 34, Flavonifractor
#> 2024-06-26 14:28:40.953332 INFO::Fitting model to feature number 35, Fusicatenibacter
#> 2024-06-26 14:28:40.957328 INFO::Fitting model to feature number 36, Fusobacterium
#> 2024-06-26 14:28:40.961436 INFO::Fitting model to feature number 37, Gemella
#> 2024-06-26 14:28:40.965453 INFO::Fitting model to feature number 38, Gordonibacter
#> 2024-06-26 14:28:40.96949 INFO::Fitting model to feature number 39, Granulicatella
#> 2024-06-26 14:28:40.973467 INFO::Fitting model to feature number 40, Haemophilus
#> 2024-06-26 14:28:40.977459 INFO::Fitting model to feature number 41, Holdemania
#> 2024-06-26 14:28:40.981442 INFO::Fitting model to feature number 42, Hungatella
#> 2024-06-26 14:28:40.985445 INFO::Fitting model to feature number 43, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.
#> 2024-06-26 14:28:40.98942 INFO::Fitting model to feature number 44, Intestinibacter
#> 2024-06-26 14:28:40.993426 INFO::Fitting model to feature number 45, Intestinimonas
#> 2024-06-26 14:28:40.997452 INFO::Fitting model to feature number 46, Klebsiella
#> 2024-06-26 14:28:41.001512 INFO::Fitting model to feature number 47, Lachnoclostridium
#> 2024-06-26 14:28:41.005536 INFO::Fitting model to feature number 48, Lachnospira
#> 2024-06-26 14:28:41.009571 INFO::Fitting model to feature number 49, Lachnospiraceae.ND3007.group
#> 2024-06-26 14:28:41.013596 INFO::Fitting model to feature number 50, Lachnospiraceae.NK4A136.group
#> 2024-06-26 14:28:41.017629 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.001
#> 2024-06-26 14:28:41.021626 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.004
#> 2024-06-26 14:28:41.025673 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.009
#> 2024-06-26 14:28:41.029669 INFO::Fitting model to feature number 54, Lachnospiraceae.UCG.010
#> 2024-06-26 14:28:41.033671 INFO::Fitting model to feature number 55, Lactobacillus
#> 2024-06-26 14:28:41.037662 INFO::Fitting model to feature number 56, Lactococcus
#> 2024-06-26 14:28:41.041682 INFO::Fitting model to feature number 57, Mannheimia
#> 2024-06-26 14:28:41.045662 INFO::Fitting model to feature number 58, Megasphaera
#> 2024-06-26 14:28:41.049743 INFO::Fitting model to feature number 59, Monoglobus
#> 2024-06-26 14:28:41.053806 INFO::Fitting model to feature number 60, Neisseria
#> 2024-06-26 14:28:41.057818 INFO::Fitting model to feature number 61, Odoribacter
#> 2024-06-26 14:28:41.0618 INFO::Fitting model to feature number 62, Oscillibacter
#> 2024-06-26 14:28:41.065805 INFO::Fitting model to feature number 63, Oscillospira
#> 2024-06-26 14:28:41.084124 INFO::Fitting model to feature number 64, Parabacteroides
#> 2024-06-26 14:28:41.088232 INFO::Fitting model to feature number 65, Parasutterella
#> 2024-06-26 14:28:41.092295 INFO::Fitting model to feature number 66, Prevotella
#> 2024-06-26 14:28:41.096398 INFO::Fitting model to feature number 67, Pseudomonas
#> 2024-06-26 14:28:41.100432 INFO::Fitting model to feature number 68, Romboutsia
#> 2024-06-26 14:28:41.104519 INFO::Fitting model to feature number 69, Roseburia
#> 2024-06-26 14:28:41.108566 INFO::Fitting model to feature number 70, Rothia
#> 2024-06-26 14:28:41.112616 INFO::Fitting model to feature number 71, Ruminococcus
#> 2024-06-26 14:28:41.116641 INFO::Fitting model to feature number 72, Sellimonas
#> 2024-06-26 14:28:41.120684 INFO::Fitting model to feature number 73, Solobacterium
#> 2024-06-26 14:28:41.124795 INFO::Fitting model to feature number 74, Staphylococcus
#> 2024-06-26 14:28:41.128836 INFO::Fitting model to feature number 75, Streptococcus
#> 2024-06-26 14:28:41.132886 INFO::Fitting model to feature number 76, Subdoligranulum
#> 2024-06-26 14:28:41.13692 INFO::Fitting model to feature number 77, Sutterella
#> 2024-06-26 14:28:41.14095 INFO::Fitting model to feature number 78, Terrisporobacter
#> 2024-06-26 14:28:41.144997 INFO::Fitting model to feature number 79, Turicibacter
#> 2024-06-26 14:28:41.149074 INFO::Fitting model to feature number 80, Tuzzerella
#> 2024-06-26 14:28:41.153121 INFO::Fitting model to feature number 81, Tyzzerella
#> 2024-06-26 14:28:41.157104 INFO::Fitting model to feature number 82, UBA1819
#> 2024-06-26 14:28:41.161209 INFO::Fitting model to feature number 83, UCG.002
#> 2024-06-26 14:28:41.165295 INFO::Fitting model to feature number 84, UCG.003
#> 2024-06-26 14:28:41.169356 INFO::Fitting model to feature number 85, UCG.005
#> 2024-06-26 14:28:41.173405 INFO::Fitting model to feature number 86, Veillonella
#> 2024-06-26 14:28:41.177471 INFO::Fitting model to feature number 87, X.Clostridium..innocuum.group
#> 2024-06-26 14:28:41.18154 INFO::Fitting model to feature number 88, X.Eubacterium..eligens.group
#> 2024-06-26 14:28:41.185596 INFO::Fitting model to feature number 89, X.Eubacterium..fissicatena.group
#> 2024-06-26 14:28:41.189681 INFO::Fitting model to feature number 90, X.Eubacterium..hallii.group
#> 2024-06-26 14:28:41.193724 INFO::Fitting model to feature number 91, X.Eubacterium..siraeum.group
#> 2024-06-26 14:28:41.197759 INFO::Fitting model to feature number 92, X.Eubacterium..ventriosum.group
#> 2024-06-26 14:28:41.201808 INFO::Fitting model to feature number 93, X.Eubacterium..xylanophilum.group
#> 2024-06-26 14:28:41.205849 INFO::Fitting model to feature number 94, X.Ruminococcus..gauvreauii.group
#> 2024-06-26 14:28:41.209905 INFO::Fitting model to feature number 95, X.Ruminococcus..gnavus.group
#> 2024-06-26 14:28:41.213941 INFO::Fitting model to feature number 96, X.Ruminococcus..torques.group
#> 2024-06-26 14:28:41.218005 INFO::Fitting model to feature number 97, unclassified.Chloroplast
#> 2024-06-26 14:28:41.222025 INFO::Fitting model to feature number 98, unclassified.Clostridia.UCG.014
#> 2024-06-26 14:28:41.226057 INFO::Fitting model to feature number 99, unclassified.Clostridia
#> 2024-06-26 14:28:41.230049 INFO::Fitting model to feature number 100, unclassified.Clostridia.vadinBB60.group
#> 2024-06-26 14:28:41.234057 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae
#> 2024-06-26 14:28:41.238059 INFO::Fitting model to feature number 102, unclassified.Mitochondria
#> 2024-06-26 14:28:41.242108 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae
#> 2024-06-26 14:28:41.246079 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus
#> 2024-06-26 14:28:41.250127 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales
#> 2024-06-26 14:28:41.254118 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae
#> 2024-06-26 14:28:41.258148 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group
#> 2024-06-26 14:28:41.273535 INFO::Counting total values for each feature
#> 2024-06-26 14:28:41.278737 INFO::Writing filtered data to file /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/features/filtered_data.tsv
#> 2024-06-26 14:28:41.462559 INFO::Writing filtered, normalized data to file /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/features/filtered_data_norm.tsv
#> 2024-06-26 14:28:41.651835 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/features/filtered_data_norm_transformed.tsv
#> 2024-06-26 14:28:41.956156 INFO::Writing residuals to file /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/fits/residuals.rds
#> 2024-06-26 14:28:42.016491 INFO::Writing fitted values to file /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/fits/fitted.rds
#> 2024-06-26 14:28:42.036554 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/all_results.tsv
#> 2024-06-26 14:28:42.038353 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d66d23efe8/significant_results.tsv

## this case of categorical variables also has a 'short cut'
diffAbundOutput <- MicrobiomeDB::differentialAbundance(
       getCollection(
  microbiomeData::DiabImmune, 
  '16S (V4) Genus (Relative taxonomic abundance analysis)'), 
       "country", 
       groupA = "Russia",
       groupB = c("Finland","Estonia"),
       method='Maaslin2', 
       verbose=FALSE
)
#> [1] "Creating output folder"
#> [1] "Creating output feature tables folder"
#> [1] "Creating output fits folder"
#> 2024-06-26 14:28:43.127976 INFO::Writing function arguments to log file
#> 2024-06-26 14:28:43.131734 INFO::Verifying options selected are valid
#> 2024-06-26 14:28:43.132289 INFO::Determining format of input files
#> 2024-06-26 14:28:43.134282 INFO::Input format is data samples as rows and metadata samples as rows
#> 2024-06-26 14:28:43.149363 INFO::Formula for fixed effects: expr ~  country
#> 2024-06-26 14:28:43.150139 INFO::Filter data based on min abundance and min prevalence
#> 2024-06-26 14:28:43.150615 INFO::Total samples in data: 3184
#> 2024-06-26 14:28:43.151061 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000
#> 2024-06-26 14:28:43.171192 INFO::Total filtered features: 564
#> 2024-06-26 14:28:43.172182 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Propionimicrobium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis..EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_., unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_., unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97
#> 2024-06-26 14:28:43.179709 INFO::Total filtered features with variance filtering: 0
#> 2024-06-26 14:28:43.180287 INFO::Filtered feature names from variance filtering:
#> 2024-06-26 14:28:43.180765 INFO::Running selected normalization method: TSS
#> 2024-06-26 14:28:43.243906 INFO::Applying z-score to standardize continuous metadata
#> 2024-06-26 14:28:43.246866 INFO::Running selected transform method: LOG
#> 2024-06-26 14:28:43.320673 INFO::Running selected analysis method: LM
#> 2024-06-26 14:28:43.321437 INFO::Fitting model to feature number 1, Actinomyces
#> 2024-06-26 14:28:43.326268 INFO::Fitting model to feature number 2, Agathobacter
#> 2024-06-26 14:28:43.330703 INFO::Fitting model to feature number 3, Akkermansia
#> 2024-06-26 14:28:43.335146 INFO::Fitting model to feature number 4, Alistipes
#> 2024-06-26 14:28:43.339552 INFO::Fitting model to feature number 5, Anaerostipes
#> 2024-06-26 14:28:43.343972 INFO::Fitting model to feature number 6, Atopobium
#> 2024-06-26 14:28:43.348365 INFO::Fitting model to feature number 7, Bacteroides
#> 2024-06-26 14:28:43.352742 INFO::Fitting model to feature number 8, Barnesiella
#> 2024-06-26 14:28:43.357127 INFO::Fitting model to feature number 9, Bifidobacterium
#> 2024-06-26 14:28:43.361506 INFO::Fitting model to feature number 10, Bilophila
#> 2024-06-26 14:28:43.365896 INFO::Fitting model to feature number 11, Blautia
#> 2024-06-26 14:28:43.370307 INFO::Fitting model to feature number 12, Butyricicoccus
#> 2024-06-26 14:28:43.374693 INFO::Fitting model to feature number 13, CAG.352
#> 2024-06-26 14:28:43.379073 INFO::Fitting model to feature number 14, Campylobacter
#> 2024-06-26 14:28:43.383432 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group
#> 2024-06-26 14:28:43.387801 INFO::Fitting model to feature number 16, Clostridioides
#> 2024-06-26 14:28:43.392164 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1
#> 2024-06-26 14:28:43.39651 INFO::Fitting model to feature number 18, Colidextribacter
#> 2024-06-26 14:28:43.400849 INFO::Fitting model to feature number 19, Collinsella
#> 2024-06-26 14:28:43.405211 INFO::Fitting model to feature number 20, Coprobacillus
#> 2024-06-26 14:28:43.409571 INFO::Fitting model to feature number 21, Coprococcus
#> 2024-06-26 14:28:43.4139 INFO::Fitting model to feature number 22, DTU089
#> 2024-06-26 14:28:43.418257 INFO::Fitting model to feature number 23, Dialister
#> 2024-06-26 14:28:43.422618 INFO::Fitting model to feature number 24, Dorea
#> 2024-06-26 14:28:43.426983 INFO::Fitting model to feature number 25, Eggerthella
#> 2024-06-26 14:28:43.431316 INFO::Fitting model to feature number 26, Eisenbergiella
#> 2024-06-26 14:28:43.43571 INFO::Fitting model to feature number 27, Enterococcus
#> 2024-06-26 14:28:43.440039 INFO::Fitting model to feature number 28, Erysipelatoclostridium
#> 2024-06-26 14:28:43.444412 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003
#> 2024-06-26 14:28:43.448776 INFO::Fitting model to feature number 30, Escherichia.Shigella
#> 2024-06-26 14:28:43.453133 INFO::Fitting model to feature number 31, Faecalibacterium
#> 2024-06-26 14:28:43.457487 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group
#> 2024-06-26 14:28:43.461858 INFO::Fitting model to feature number 33, Flavonifractor
#> 2024-06-26 14:28:43.466208 INFO::Fitting model to feature number 34, Fusicatenibacter
#> 2024-06-26 14:28:43.470591 INFO::Fitting model to feature number 35, Fusobacterium
#> 2024-06-26 14:28:43.474938 INFO::Fitting model to feature number 36, Gemella
#> 2024-06-26 14:28:43.479327 INFO::Fitting model to feature number 37, Granulicatella
#> 2024-06-26 14:28:43.4837 INFO::Fitting model to feature number 38, Haemophilus
#> 2024-06-26 14:28:43.488125 INFO::Fitting model to feature number 39, Holdemania
#> 2024-06-26 14:28:43.49248 INFO::Fitting model to feature number 40, Hungatella
#> 2024-06-26 14:28:43.496834 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.
#> 2024-06-26 14:28:43.501238 INFO::Fitting model to feature number 42, Intestinibacter
#> 2024-06-26 14:28:43.505665 INFO::Fitting model to feature number 43, Intestinimonas
#> 2024-06-26 14:28:43.510047 INFO::Fitting model to feature number 44, Klebsiella
#> 2024-06-26 14:28:43.514436 INFO::Fitting model to feature number 45, Lachnoclostridium
#> 2024-06-26 14:28:43.518797 INFO::Fitting model to feature number 46, Lachnospira
#> 2024-06-26 14:28:43.523234 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group
#> 2024-06-26 14:28:43.527607 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group
#> 2024-06-26 14:28:43.532026 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group
#> 2024-06-26 14:28:43.53642 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001
#> 2024-06-26 14:28:43.540777 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004
#> 2024-06-26 14:28:43.545163 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009
#> 2024-06-26 14:28:43.549495 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010
#> 2024-06-26 14:28:43.553842 INFO::Fitting model to feature number 54, Lactobacillus
#> 2024-06-26 14:28:43.558252 INFO::Fitting model to feature number 55, Lactococcus
#> 2024-06-26 14:28:43.562608 INFO::Fitting model to feature number 56, Mannheimia
#> 2024-06-26 14:28:43.566989 INFO::Fitting model to feature number 57, Megasphaera
#> 2024-06-26 14:28:43.571387 INFO::Fitting model to feature number 58, Monoglobus
#> 2024-06-26 14:28:43.575753 INFO::Fitting model to feature number 59, Neisseria
#> 2024-06-26 14:28:43.58014 INFO::Fitting model to feature number 60, Odoribacter
#> 2024-06-26 14:28:43.584507 INFO::Fitting model to feature number 61, Oscillibacter
#> 2024-06-26 14:28:43.588952 INFO::Fitting model to feature number 62, Oscillospira
#> 2024-06-26 14:28:43.593298 INFO::Fitting model to feature number 63, Parabacteroides
#> 2024-06-26 14:28:43.597639 INFO::Fitting model to feature number 64, Parasutterella
#> 2024-06-26 14:28:43.60201 INFO::Fitting model to feature number 65, Prevotella
#> 2024-06-26 14:28:43.606395 INFO::Fitting model to feature number 66, Pseudomonas
#> 2024-06-26 14:28:43.610715 INFO::Fitting model to feature number 67, Romboutsia
#> 2024-06-26 14:28:43.615073 INFO::Fitting model to feature number 68, Roseburia
#> 2024-06-26 14:28:43.619457 INFO::Fitting model to feature number 69, Rothia
#> 2024-06-26 14:28:43.623802 INFO::Fitting model to feature number 70, Ruminococcus
#> 2024-06-26 14:28:43.628179 INFO::Fitting model to feature number 71, Sellimonas
#> 2024-06-26 14:28:43.632594 INFO::Fitting model to feature number 72, Solobacterium
#> 2024-06-26 14:28:43.636945 INFO::Fitting model to feature number 73, Staphylococcus
#> 2024-06-26 14:28:43.641282 INFO::Fitting model to feature number 74, Streptococcus
#> 2024-06-26 14:28:43.645658 INFO::Fitting model to feature number 75, Subdoligranulum
#> 2024-06-26 14:28:43.650006 INFO::Fitting model to feature number 76, Sutterella
#> 2024-06-26 14:28:43.654366 INFO::Fitting model to feature number 77, Terrisporobacter
#> 2024-06-26 14:28:43.658754 INFO::Fitting model to feature number 78, Turicibacter
#> 2024-06-26 14:28:43.663152 INFO::Fitting model to feature number 79, Tuzzerella
#> 2024-06-26 14:28:43.667567 INFO::Fitting model to feature number 80, Tyzzerella
#> 2024-06-26 14:28:43.671877 INFO::Fitting model to feature number 81, UBA1819
#> 2024-06-26 14:28:43.676272 INFO::Fitting model to feature number 82, UCG.002
#> 2024-06-26 14:28:43.680634 INFO::Fitting model to feature number 83, UCG.003
#> 2024-06-26 14:28:43.684961 INFO::Fitting model to feature number 84, UCG.005
#> 2024-06-26 14:28:43.689335 INFO::Fitting model to feature number 85, Veillonella
#> 2024-06-26 14:28:43.69375 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group
#> 2024-06-26 14:28:43.698128 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group
#> 2024-06-26 14:28:43.702481 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group
#> 2024-06-26 14:28:43.706848 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group
#> 2024-06-26 14:28:43.711264 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group
#> 2024-06-26 14:28:43.715627 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group
#> 2024-06-26 14:28:43.719963 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group
#> 2024-06-26 14:28:43.724378 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group
#> 2024-06-26 14:28:43.728764 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group
#> 2024-06-26 14:28:43.747637 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group
#> 2024-06-26 14:28:43.752469 INFO::Fitting model to feature number 96, unclassified.Chloroplast
#> 2024-06-26 14:28:43.757132 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014
#> 2024-06-26 14:28:43.76175 INFO::Fitting model to feature number 98, unclassified.Clostridia
#> 2024-06-26 14:28:43.766402 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group
#> 2024-06-26 14:28:43.770905 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales
#> 2024-06-26 14:28:43.775431 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae
#> 2024-06-26 14:28:43.779952 INFO::Fitting model to feature number 102, unclassified.Mitochondria
#> 2024-06-26 14:28:43.784541 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae
#> 2024-06-26 14:28:43.789099 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus
#> 2024-06-26 14:28:43.793588 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales
#> 2024-06-26 14:28:43.798114 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae
#> 2024-06-26 14:28:43.802578 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group
#> 2024-06-26 14:28:43.818466 INFO::Counting total values for each feature
#> 2024-06-26 14:28:43.823811 INFO::Writing filtered data to file /tmp/Rtmp1DvrdC/maaslin17d6502010b7/features/filtered_data.tsv
#> 2024-06-26 14:28:44.038675 INFO::Writing filtered, normalized data to file /tmp/Rtmp1DvrdC/maaslin17d6502010b7/features/filtered_data_norm.tsv
#> 2024-06-26 14:28:44.258121 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp1DvrdC/maaslin17d6502010b7/features/filtered_data_norm_transformed.tsv
#> 2024-06-26 14:28:44.618222 INFO::Writing residuals to file /tmp/Rtmp1DvrdC/maaslin17d6502010b7/fits/residuals.rds
#> 2024-06-26 14:28:44.688576 INFO::Writing fitted values to file /tmp/Rtmp1DvrdC/maaslin17d6502010b7/fits/fitted.rds
#> 2024-06-26 14:28:44.712056 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d6502010b7/all_results.tsv
#> 2024-06-26 14:28:44.713945 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d6502010b7/significant_results.tsv

## a categorical variable with 2 values
diffAbundOutput <- MicrobiomeDB::differentialAbundance(
       getCollection(
  microbiomeData::DiabImmune, 
  '16S (V4) Genus (Relative taxonomic abundance analysis)'),
       "delivery_mode",
       method='Maaslin2', 
       verbose=FALSE
) 
#> [1] "Creating output folder"
#> [1] "Creating output feature tables folder"
#> [1] "Creating output fits folder"
#> 2024-06-26 14:28:45.030735 INFO::Writing function arguments to log file
#> 2024-06-26 14:28:45.034496 INFO::Verifying options selected are valid
#> 2024-06-26 14:28:45.035025 INFO::Determining format of input files
#> 2024-06-26 14:28:45.036716 INFO::Input format is data samples as rows and metadata samples as rows
#> 2024-06-26 14:28:45.052018 INFO::Formula for fixed effects: expr ~  delivery_mode
#> 2024-06-26 14:28:45.052823 INFO::Filter data based on min abundance and min prevalence
#> 2024-06-26 14:28:45.053312 INFO::Total samples in data: 3184
#> 2024-06-26 14:28:45.053761 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000
#> 2024-06-26 14:28:45.073807 INFO::Total filtered features: 564
#> 2024-06-26 14:28:45.074777 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Propionimicrobium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis..EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_., unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_., unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97
#> 2024-06-26 14:28:45.082285 INFO::Total filtered features with variance filtering: 0
#> 2024-06-26 14:28:45.08281 INFO::Filtered feature names from variance filtering:
#> 2024-06-26 14:28:45.083261 INFO::Running selected normalization method: TSS
#> 2024-06-26 14:28:45.144733 INFO::Applying z-score to standardize continuous metadata
#> 2024-06-26 14:28:45.1477 INFO::Running selected transform method: LOG
#> 2024-06-26 14:28:45.221943 INFO::Running selected analysis method: LM
#> 2024-06-26 14:28:45.222742 INFO::Fitting model to feature number 1, Actinomyces
#> 2024-06-26 14:28:45.227569 INFO::Fitting model to feature number 2, Agathobacter
#> 2024-06-26 14:28:45.231991 INFO::Fitting model to feature number 3, Akkermansia
#> 2024-06-26 14:28:45.236442 INFO::Fitting model to feature number 4, Alistipes
#> 2024-06-26 14:28:45.240847 INFO::Fitting model to feature number 5, Anaerostipes
#> 2024-06-26 14:28:45.245233 INFO::Fitting model to feature number 6, Atopobium
#> 2024-06-26 14:28:45.249611 INFO::Fitting model to feature number 7, Bacteroides
#> 2024-06-26 14:28:45.254002 INFO::Fitting model to feature number 8, Barnesiella
#> 2024-06-26 14:28:45.258443 INFO::Fitting model to feature number 9, Bifidobacterium
#> 2024-06-26 14:28:45.26284 INFO::Fitting model to feature number 10, Bilophila
#> 2024-06-26 14:28:45.267248 INFO::Fitting model to feature number 11, Blautia
#> 2024-06-26 14:28:45.271621 INFO::Fitting model to feature number 12, Butyricicoccus
#> 2024-06-26 14:28:45.276024 INFO::Fitting model to feature number 13, CAG.352
#> 2024-06-26 14:28:45.280457 INFO::Fitting model to feature number 14, Campylobacter
#> 2024-06-26 14:28:45.284834 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group
#> 2024-06-26 14:28:45.289253 INFO::Fitting model to feature number 16, Clostridioides
#> 2024-06-26 14:28:45.293635 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1
#> 2024-06-26 14:28:45.29809 INFO::Fitting model to feature number 18, Colidextribacter
#> 2024-06-26 14:28:45.302502 INFO::Fitting model to feature number 19, Collinsella
#> 2024-06-26 14:28:45.306921 INFO::Fitting model to feature number 20, Coprobacillus
#> 2024-06-26 14:28:45.311322 INFO::Fitting model to feature number 21, Coprococcus
#> 2024-06-26 14:28:45.315756 INFO::Fitting model to feature number 22, DTU089
#> 2024-06-26 14:28:45.3202 INFO::Fitting model to feature number 23, Dialister
#> 2024-06-26 14:28:45.324611 INFO::Fitting model to feature number 24, Dorea
#> 2024-06-26 14:28:45.329044 INFO::Fitting model to feature number 25, Eggerthella
#> 2024-06-26 14:28:45.333427 INFO::Fitting model to feature number 26, Eisenbergiella
#> 2024-06-26 14:28:45.337855 INFO::Fitting model to feature number 27, Enterococcus
#> 2024-06-26 14:28:45.342296 INFO::Fitting model to feature number 28, Erysipelatoclostridium
#> 2024-06-26 14:28:45.346755 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003
#> 2024-06-26 14:28:45.35114 INFO::Fitting model to feature number 30, Escherichia.Shigella
#> 2024-06-26 14:28:45.355578 INFO::Fitting model to feature number 31, Faecalibacterium
#> 2024-06-26 14:28:45.360015 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group
#> 2024-06-26 14:28:45.364446 INFO::Fitting model to feature number 33, Flavonifractor
#> 2024-06-26 14:28:45.368871 INFO::Fitting model to feature number 34, Fusicatenibacter
#> 2024-06-26 14:28:45.373266 INFO::Fitting model to feature number 35, Fusobacterium
#> 2024-06-26 14:28:45.377665 INFO::Fitting model to feature number 36, Gemella
#> 2024-06-26 14:28:45.382061 INFO::Fitting model to feature number 37, Granulicatella
#> 2024-06-26 14:28:45.386512 INFO::Fitting model to feature number 38, Haemophilus
#> 2024-06-26 14:28:45.390942 INFO::Fitting model to feature number 39, Holdemania
#> 2024-06-26 14:28:45.395352 INFO::Fitting model to feature number 40, Hungatella
#> 2024-06-26 14:28:45.399747 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.
#> 2024-06-26 14:28:45.404183 INFO::Fitting model to feature number 42, Intestinibacter
#> 2024-06-26 14:28:45.408635 INFO::Fitting model to feature number 43, Intestinimonas
#> 2024-06-26 14:28:45.413008 INFO::Fitting model to feature number 44, Klebsiella
#> 2024-06-26 14:28:45.417498 INFO::Fitting model to feature number 45, Lachnoclostridium
#> 2024-06-26 14:28:45.421927 INFO::Fitting model to feature number 46, Lachnospira
#> 2024-06-26 14:28:45.426366 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group
#> 2024-06-26 14:28:45.430767 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group
#> 2024-06-26 14:28:45.435181 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group
#> 2024-06-26 14:28:45.439575 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001
#> 2024-06-26 14:28:45.443948 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004
#> 2024-06-26 14:28:45.448364 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009
#> 2024-06-26 14:28:45.452738 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010
#> 2024-06-26 14:28:45.457144 INFO::Fitting model to feature number 54, Lactobacillus
#> 2024-06-26 14:28:45.461531 INFO::Fitting model to feature number 55, Lactococcus
#> 2024-06-26 14:28:45.46593 INFO::Fitting model to feature number 56, Mannheimia
#> 2024-06-26 14:28:45.470306 INFO::Fitting model to feature number 57, Megasphaera
#> 2024-06-26 14:28:45.474727 INFO::Fitting model to feature number 58, Monoglobus
#> 2024-06-26 14:28:45.479089 INFO::Fitting model to feature number 59, Neisseria
#> 2024-06-26 14:28:45.483461 INFO::Fitting model to feature number 60, Odoribacter
#> 2024-06-26 14:28:45.487833 INFO::Fitting model to feature number 61, Oscillibacter
#> 2024-06-26 14:28:45.492261 INFO::Fitting model to feature number 62, Oscillospira
#> 2024-06-26 14:28:45.496638 INFO::Fitting model to feature number 63, Parabacteroides
#> 2024-06-26 14:28:45.501028 INFO::Fitting model to feature number 64, Parasutterella
#> 2024-06-26 14:28:45.505471 INFO::Fitting model to feature number 65, Prevotella
#> 2024-06-26 14:28:45.509887 INFO::Fitting model to feature number 66, Pseudomonas
#> 2024-06-26 14:28:45.528445 INFO::Fitting model to feature number 67, Romboutsia
#> 2024-06-26 14:28:45.533027 INFO::Fitting model to feature number 68, Roseburia
#> 2024-06-26 14:28:45.537522 INFO::Fitting model to feature number 69, Rothia
#> 2024-06-26 14:28:45.542023 INFO::Fitting model to feature number 70, Ruminococcus
#> 2024-06-26 14:28:45.546551 INFO::Fitting model to feature number 71, Sellimonas
#> 2024-06-26 14:28:45.55106 INFO::Fitting model to feature number 72, Solobacterium
#> 2024-06-26 14:28:45.555521 INFO::Fitting model to feature number 73, Staphylococcus
#> 2024-06-26 14:28:45.56002 INFO::Fitting model to feature number 74, Streptococcus
#> 2024-06-26 14:28:45.564568 INFO::Fitting model to feature number 75, Subdoligranulum
#> 2024-06-26 14:28:45.569041 INFO::Fitting model to feature number 76, Sutterella
#> 2024-06-26 14:28:45.573512 INFO::Fitting model to feature number 77, Terrisporobacter
#> 2024-06-26 14:28:45.578003 INFO::Fitting model to feature number 78, Turicibacter
#> 2024-06-26 14:28:45.582521 INFO::Fitting model to feature number 79, Tuzzerella
#> 2024-06-26 14:28:45.586948 INFO::Fitting model to feature number 80, Tyzzerella
#> 2024-06-26 14:28:45.591408 INFO::Fitting model to feature number 81, UBA1819
#> 2024-06-26 14:28:45.595887 INFO::Fitting model to feature number 82, UCG.002
#> 2024-06-26 14:28:45.600371 INFO::Fitting model to feature number 83, UCG.003
#> 2024-06-26 14:28:45.604836 INFO::Fitting model to feature number 84, UCG.005
#> 2024-06-26 14:28:45.609287 INFO::Fitting model to feature number 85, Veillonella
#> 2024-06-26 14:28:45.613813 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group
#> 2024-06-26 14:28:45.618253 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group
#> 2024-06-26 14:28:45.622738 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group
#> 2024-06-26 14:28:45.627226 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group
#> 2024-06-26 14:28:45.631691 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group
#> 2024-06-26 14:28:45.636136 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group
#> 2024-06-26 14:28:45.640585 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group
#> 2024-06-26 14:28:45.645023 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group
#> 2024-06-26 14:28:45.64945 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group
#> 2024-06-26 14:28:45.653943 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group
#> 2024-06-26 14:28:45.658385 INFO::Fitting model to feature number 96, unclassified.Chloroplast
#> 2024-06-26 14:28:45.662812 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014
#> 2024-06-26 14:28:45.667282 INFO::Fitting model to feature number 98, unclassified.Clostridia
#> 2024-06-26 14:28:45.67169 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group
#> 2024-06-26 14:28:45.676087 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales
#> 2024-06-26 14:28:45.680557 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae
#> 2024-06-26 14:28:45.685022 INFO::Fitting model to feature number 102, unclassified.Mitochondria
#> 2024-06-26 14:28:45.689482 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae
#> 2024-06-26 14:28:45.694057 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus
#> 2024-06-26 14:28:45.69851 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales
#> 2024-06-26 14:28:45.702954 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae
#> 2024-06-26 14:28:45.707375 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group
#> 2024-06-26 14:28:45.723889 INFO::Counting total values for each feature
#> 2024-06-26 14:28:45.729269 INFO::Writing filtered data to file /tmp/Rtmp1DvrdC/maaslin17d6110ade45/features/filtered_data.tsv
#> 2024-06-26 14:28:45.947228 INFO::Writing filtered, normalized data to file /tmp/Rtmp1DvrdC/maaslin17d6110ade45/features/filtered_data_norm.tsv
#> 2024-06-26 14:28:46.169906 INFO::Writing filtered, normalized, transformed data to file /tmp/Rtmp1DvrdC/maaslin17d6110ade45/features/filtered_data_norm_transformed.tsv
#> 2024-06-26 14:28:46.530654 INFO::Writing residuals to file /tmp/Rtmp1DvrdC/maaslin17d6110ade45/fits/residuals.rds
#> 2024-06-26 14:28:46.600953 INFO::Writing fitted values to file /tmp/Rtmp1DvrdC/maaslin17d6110ade45/fits/fitted.rds
#> 2024-06-26 14:28:46.625121 INFO::Writing all results to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d6110ade45/all_results.tsv
#> 2024-06-26 14:28:46.626922 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/Rtmp1DvrdC/maaslin17d6110ade45/significant_results.tsv