Get the variables in the Microbiome Dataset by their names. The requested variables could belong to any collection or to the metadata. The returned data.table will contain the requested variables as columns and any appropriate identifiers. If one of the requested variables cannot be returned, a warning will be printed.
Arguments
- object
A Microbiome Dataset
- variables
The names of the variables to return. This should be a named list where the names are collection names and the values are variable names for that collection. For the case of metadata variables, the name should be "metadata".
Examples
getCollectionVariableNames(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)"
)
#> [1] "28-4"
#> [2] "Abiotrophia"
#> [3] "Acetanaerobacterium"
#> [4] "Acetobacter"
#> [5] "Achromobacter"
#> [6] "Acidaminococcus"
#> [7] "Acidibacter"
#> [8] "Acidiphilium"
#> [9] "Acidipropionibacterium"
#> [10] "Acidocella"
#> [11] "Acidovorax"
#> [12] "Acinetobacter"
#> [13] "Actinobacillus"
#> [14] "Actinobaculum"
#> [15] "Actinomyces"
#> [16] "Actinotignum"
#> [17] "Adlercreutzia"
#> [18] "Aerococcus"
#> [19] "Aeromonas"
#> [20] "Afipia"
#> [21] "Agathobacter"
#> [22] "Aggregatibacter"
#> [23] "Akkermansia"
#> [24] "Alcaligenes"
#> [25] "Alicycliphilus"
#> [26] "Alistipes"
#> [27] "Allisonella"
#> [28] "Allobaculum"
#> [29] "Alloprevotella"
#> [30] "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"
#> [31] "Alloscardovia"
#> [32] "Amaricoccus"
#> [33] "Amnibacterium"
#> [34] "Anaerobium"
#> [35] "Anaerocolumna"
#> [36] "Anaerofilum"
#> [37] "Anaerofustis"
#> [38] "Anaeroglobus"
#> [39] "Anaeromyxobacter"
#> [40] "Anaeroplasma"
#> [41] "Anaerosporobacter"
#> [42] "Anaerosporomusa"
#> [43] "Anaerostignum"
#> [44] "Anaerostipes"
#> [45] "Anaerotruncus"
#> [46] "Angelakisella"
#> [47] "Angustibacter"
#> [48] "Anoxybacillus"
#> [49] "Aquabacterium"
#> [50] "Aquamonas"
#> [51] "Arcanobacterium"
#> [52] "Arcticibacter"
#> [53] "Asaccharospora"
#> [54] "Asaia"
#> [55] "Asinibacterium"
#> [56] "Asteroleplasma"
#> [57] "Asticcacaulis"
#> [58] "Atopobium"
#> [59] "Aureimonas"
#> [60] "Azospira"
#> [61] "Bacillus"
#> [62] "Bacteriovorax"
#> [63] "Bacteroides"
#> [64] "Barnesiella"
#> [65] "Bdellovibrio"
#> [66] "Belnapia"
#> [67] "Bergeyella"
#> [68] "Bifidobacterium"
#> [69] "Bilophila"
#> [70] "Blastomonas"
#> [71] "Blautia"
#> [72] "Bordetella"
#> [73] "Bosea"
#> [74] "Brachybacterium"
#> [75] "Bradyrhizobium"
#> [76] "Brevibacterium"
#> [77] "Brevundimonas"
#> [78] "Brucella"
#> [79] "Bulleidia"
#> [80] "Burkholderia-Caballeronia-Paraburkholderia"
#> [81] "Buttiauxella"
#> [82] "Butyricicoccus"
#> [83] "Butyricimonas"
#> [84] "CAG-352"
#> [85] "CAG-56"
#> [86] "CAG-873"
#> [87] "CHKCI001"
#> [88] "CHKCI002"
#> [89] "CL500-29 marine group"
#> [90] "Caloribacterium"
#> [91] "Campylobacter"
#> [92] "Candidatus Arthromitus"
#> [93] "Candidatus Metachlamydia"
#> [94] "Candidatus Obscuribacter"
#> [95] "Candidatus Phytoplasma"
#> [96] "Candidatus Soleaferrea"
#> [97] "Candidatus Stoquefichus"
#> [98] "Capnocytophaga"
#> [99] "Caproiciproducens"
#> [100] "Cardiobacterium"
#> [101] "Carnobacterium"
#> [102] "Caryophanon"
#> [103] "Castellaniella"
#> [104] "Catabacter"
#> [105] "Catenibacillus"
#> [106] "Catenibacterium"
#> [107] "Catenisphaera"
#> [108] "Catonella"
#> [109] "Caulobacter"
#> [110] "Cellulomonas"
#> [111] "Cellulosilyticum"
#> [112] "Cellvibrio"
#> [113] "Centipeda"
#> [114] "Cetobacterium"
#> [115] "Christensenella"
#> [116] "Christensenellaceae R-7 group"
#> [117] "Chryseobacterium"
#> [118] "Chryseomicrobium"
#> [119] "Chungangia"
#> [120] "Citrobacter"
#> [121] "Clavibacter"
#> [122] "Cloacibacillus"
#> [123] "Cloacibacterium"
#> [124] "Clostridioides"
#> [125] "Clostridium sensu stricto 1"
#> [126] "Clostridium sensu stricto 12"
#> [127] "Clostridium sensu stricto 13"
#> [128] "Clostridium sensu stricto 15"
#> [129] "Clostridium sensu stricto 18"
#> [130] "Clostridium sensu stricto 2"
#> [131] "Clostridium sensu stricto 3"
#> [132] "Clostridium sensu stricto 4"
#> [133] "Clostridium sensu stricto 6"
#> [134] "Colidextribacter"
#> [135] "Collinsella"
#> [136] "Comamonas"
#> [137] "Conexibacter"
#> [138] "Conservatibacter"
#> [139] "Coprobacillus"
#> [140] "Coprobacter"
#> [141] "Coprococcus"
#> [142] "Coriobacteriaceae UCG-002"
#> [143] "Corynebacterium"
#> [144] "Cosenzaea"
#> [145] "Criibacterium"
#> [146] "Cryptobacterium"
#> [147] "Curvibacter"
#> [148] "Cutibacterium"
#> [149] "Cytophaga"
#> [150] "DNF00809"
#> [151] "DSSD61"
#> [152] "DTU089"
#> [153] "Dechloromonas"
#> [154] "Defluviicoccus"
#> [155] "Defluviitaleaceae UCG-011"
#> [156] "Delftia"
#> [157] "Denitrobacterium"
#> [158] "Dermabacter"
#> [159] "Desemzia"
#> [160] "Desulfovibrio"
#> [161] "Devosia"
#> [162] "Dialister"
#> [163] "Diaphorobacter"
#> [164] "Dickeya"
#> [165] "Dielma"
#> [166] "Dietzia"
#> [167] "Dinghuibacter"
#> [168] "Diplosphaera"
#> [169] "Dolosigranulum"
#> [170] "Dorea"
#> [171] "Duganella"
#> [172] "Dysgonomonas"
#> [173] "Edaphobaculum"
#> [174] "Eggerthella"
#> [175] "Eikenella"
#> [176] "Eisenbergiella"
#> [177] "Empedobacter"
#> [178] "Endobacter"
#> [179] "Enhydrobacter"
#> [180] "Enterobacter"
#> [181] "Enterococcus"
#> [182] "Enterorhabdus"
#> [183] "Enteroscipio"
#> [184] "Epulopiscium"
#> [185] "Erwinia"
#> [186] "Erysipelatoclostridium"
#> [187] "Erysipelotrichaceae UCG-003"
#> [188] "Erysipelotrichaceae UCG-006"
#> [189] "Escherichia/Shigella"
#> [190] "Eubacterium"
#> [191] "Exiguobacterium"
#> [192] "Extensimonas"
#> [193] "F0058"
#> [194] "F0332"
#> [195] "FD2005"
#> [196] "Facklamia"
#> [197] "Faecalibacterium"
#> [198] "Faecalicoccus"
#> [199] "Faecalitalea"
#> [200] "Falsochrobactrum"
#> [201] "Family XIII AD3011 group"
#> [202] "Family XIII UCG-001"
#> [203] "Fictibacillus"
#> [204] "Flaviflexus"
#> [205] "Flavihumibacter"
#> [206] "Flavobacterium"
#> [207] "Flavonifractor"
#> [208] "Floricoccus"
#> [209] "Fluviicola"
#> [210] "Fournierella"
#> [211] "Fretibacterium"
#> [212] "Frisingicoccus"
#> [213] "Fructobacillus"
#> [214] "Fusicatenibacter"
#> [215] "Fusobacterium"
#> [216] "GCA-900066575"
#> [217] "GCA-900066755"
#> [218] "Galbibacter"
#> [219] "Garciella"
#> [220] "Gemella"
#> [221] "Gemmata"
#> [222] "Geobacillus"
#> [223] "Gluconobacter"
#> [224] "Glutamicibacter"
#> [225] "Gordonia"
#> [226] "Gordonibacter"
#> [227] "Granulicatella"
#> [228] "Gulbenkiania"
#> [229] "Haemophilus"
#> [230] "Hafnia-Obesumbacterium"
#> [231] "Halomonas"
#> [232] "Haoranjiania"
#> [233] "Harryflintia"
#> [234] "Helicobacter"
#> [235] "Hephaestia"
#> [236] "Herbaspirillum"
#> [237] "Herbinix"
#> [238] "Holdemanella"
#> [239] "Holdemania"
#> [240] "Howardella"
#> [241] "Hungatella"
#> [242] "Hydrocarboniphaga"
#> [243] "Hydrogenophilus"
#> [244] "Hymenobacter"
#> [245] "Iamia"
#> [246] "Ignavigranum"
#> [247] "Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis]"
#> [248] "Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis]"
#> [249] "Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis]"
#> [250] "Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis]"
#> [251] "Intestinibacter"
#> [252] "Intestinimonas"
#> [253] "Janthinobacterium"
#> [254] "Jeotgalicoccus"
#> [255] "Johnsonella"
#> [256] "Kingella"
#> [257] "Klebsiella"
#> [258] "Knoellia"
#> [259] "Kocuria"
#> [260] "Kosakonia"
#> [261] "Lachnoanaerobaculum"
#> [262] "Lachnobacterium"
#> [263] "Lachnoclostridium"
#> [264] "Lachnospira"
#> [265] "Lachnospiraceae AC2044 group"
#> [266] "Lachnospiraceae FCS020 group"
#> [267] "Lachnospiraceae FE2018 group"
#> [268] "Lachnospiraceae NC2004 group"
#> [269] "Lachnospiraceae ND3007 group"
#> [270] "Lachnospiraceae NK4A136 group"
#> [271] "Lachnospiraceae UCG-001"
#> [272] "Lachnospiraceae UCG-002"
#> [273] "Lachnospiraceae UCG-003"
#> [274] "Lachnospiraceae UCG-004"
#> [275] "Lachnospiraceae UCG-008"
#> [276] "Lachnospiraceae UCG-009"
#> [277] "Lachnospiraceae UCG-010"
#> [278] "Lachnospiraceae XPB1014 group"
#> [279] "Lachnotalea"
#> [280] "Lactobacillus"
#> [281] "Lactococcus"
#> [282] "Lactonifactor"
#> [283] "Lautropia"
#> [284] "Lawsonella"
#> [285] "Legionella"
#> [286] "Leptotrichia"
#> [287] "Leuconostoc"
#> [288] "Libanicoccus"
#> [289] "Luteimonas"
#> [290] "Luteolibacter"
#> [291] "Macellibacteroides"
#> [292] "Macrococcus"
#> [293] "Mailhella"
#> [294] "Mannheimia"
#> [295] "Marinilactibacillus"
#> [296] "Marmoricola"
#> [297] "Martelella"
#> [298] "Marvinbryantia"
#> [299] "Massilia"
#> [300] "Megamonas"
#> [301] "Megasphaera"
#> [302] "Merdibacter"
#> [303] "Mesorhizobium"
#> [304] "Methanobrevibacter"
#> [305] "Methylibium"
#> [306] "Methylobacillus"
#> [307] "Methylobacterium-Methylorubrum"
#> [308] "Methylorosula"
#> [309] "Methylotenera"
#> [310] "Micrococcus"
#> [311] "Mitsuokella"
#> [312] "Mobiluncus"
#> [313] "Mogibacterium"
#> [314] "Moheibacter"
#> [315] "Mongoliitalea"
#> [316] "Monoglobus"
#> [317] "Moraxella"
#> [318] "Morganella"
#> [319] "Moryella"
#> [320] "Mucilaginibacter"
#> [321] "Muribaculum"
#> [322] "Murimonas"
#> [323] "Mycobacterium"
#> [324] "Mycoplasma"
#> [325] "Myxococcus"
#> [326] "NK4A214 group"
#> [327] "Nakamurella"
#> [328] "Nannocystis"
#> [329] "Necropsobacter"
#> [330] "Negativibacillus"
#> [331] "Negativicoccus"
#> [332] "Neisseria"
#> [333] "Neochlamydia"
#> [334] "Neomegalonema"
#> [335] "Neorhizobium"
#> [336] "Neoscardovia"
#> [337] "Nesterenkonia"
#> [338] "Nocardioides"
#> [339] "Nocardiopsis"
#> [340] "Novosphingobium"
#> [341] "Oceanivirga"
#> [342] "Oceanobacillus"
#> [343] "Ochrobactrum"
#> [344] "Odoribacter"
#> [345] "Olsenella"
#> [346] "Oribacterium"
#> [347] "Oscillibacter"
#> [348] "Oscillospira"
#> [349] "Ottowia"
#> [350] "Oxalobacter"
#> [351] "Oxobacter"
#> [352] "P3OB-42"
#> [353] "Paenibacillus"
#> [354] "Paeniclostridium"
#> [355] "Paenisporosarcina"
#> [356] "Paludicola"
#> [357] "Papillibacter"
#> [358] "Parabacteroides"
#> [359] "Paraclostridium"
#> [360] "Paracoccus"
#> [361] "Paramesorhizobium"
#> [362] "Paraprevotella"
#> [363] "Parapusillimonas"
#> [364] "Parascardovia"
#> [365] "Parasutterella"
#> [366] "Parvibacter"
#> [367] "Pasteurella"
#> [368] "Paucibacter"
#> [369] "Pediococcus"
#> [370] "Pedobacter"
#> [371] "Peptoclostridium"
#> [372] "Peptococcus"
#> [373] "Peptostreptococcus"
#> [374] "Perlucidibaca"
#> [375] "Phascolarctobacterium"
#> [376] "Phaseolibacter"
#> [377] "Phocea"
#> [378] "Phoenicibacter"
#> [379] "Phyllobacterium"
#> [380] "Piscinibacter"
#> [381] "Planifilum"
#> [382] "Plesiomonas"
#> [383] "Plot4-2H12"
#> [384] "Pluralibacter"
#> [385] "Polaromonas"
#> [386] "Porphyromonas"
#> [387] "Prevotella"
#> [388] "Prevotellaceae NK3B31 group"
#> [389] "Prevotellaceae UCG-001"
#> [390] "Propionibacterium"
#> [391] "Propionimicrobium"
#> [392] "Prosthecobacter"
#> [393] "Proteus"
#> [394] "Providencia"
#> [395] "Pseudacidovorax"
#> [396] "Pseudaminobacter"
#> [397] "Pseudocitrobacter"
#> [398] "Pseudoflavonifractor"
#> [399] "Pseudoglutamicibacter"
#> [400] "Pseudomonas"
#> [401] "Pseudoramibacter"
#> [402] "Pseudoxanthomonas"
#> [403] "Psychrobacter"
#> [404] "Pygmaiobacter"
#> [405] "Pyramidobacter"
#> [406] "Qipengyuania"
#> [407] "Ralstonia"
#> [408] "Raoultella"
#> [409] "Raoultibacter"
#> [410] "Reyranella"
#> [411] "Rhizorhapis"
#> [412] "Rhodanobacter"
#> [413] "Rhodobacter"
#> [414] "Rhodococcus"
#> [415] "Rikenella"
#> [416] "Rikenellaceae RC9 gut group"
#> [417] "Rivicola"
#> [418] "Robinsoniella"
#> [419] "Rodentibacter"
#> [420] "Romboutsia"
#> [421] "Roseburia"
#> [422] "Roseisolibacter"
#> [423] "Rothia"
#> [424] "Rubellimicrobium"
#> [425] "Ruminococcus"
#> [426] "Rummeliibacillus"
#> [427] "S5-A14a"
#> [428] "SH-PL14"
#> [429] "Saccharothrix"
#> [430] "Salinimicrobium"
#> [431] "Salinisphaera"
#> [432] "Salipaludibacillus"
#> [433] "Salmonella"
#> [434] "Sanguibacteroides"
#> [435] "Sarcina"
#> [436] "Scardovia"
#> [437] "Sedimentibacter"
#> [438] "Segetibacter"
#> [439] "Selenomonas"
#> [440] "Sellimonas"
#> [441] "Senegalimassilia"
#> [442] "Serratia"
#> [443] "Shimwellia"
#> [444] "Shuttleworthia"
#> [445] "Slackia"
#> [446] "Sneathia"
#> [447] "Solibacillus"
#> [448] "Solobacterium"
#> [449] "Sphingoaurantiacus"
#> [450] "Sphingobacterium"
#> [451] "Sphingobium"
#> [452] "Sphingomonas"
#> [453] "Sphingopyxis"
#> [454] "Sporolactobacillus"
#> [455] "Staphylococcus"
#> [456] "Stenotrophomonas"
#> [457] "Stomatobaculum"
#> [458] "Streptobacillus"
#> [459] "Streptococcus"
#> [460] "Subdoligranulum"
#> [461] "Succinatimonas"
#> [462] "Succiniclasticum"
#> [463] "Succinivibrio"
#> [464] "Sulfurospirillum"
#> [465] "Sutterella"
#> [466] "Synergistes"
#> [467] "TM7x"
#> [468] "Tannerella"
#> [469] "Tatumella"
#> [470] "Tepidimonas"
#> [471] "Tepidiphilus"
#> [472] "Terrisporobacter"
#> [473] "Tetragenococcus"
#> [474] "Thermus"
#> [475] "Timonella"
#> [476] "Tolumonas"
#> [477] "Trabulsiella"
#> [478] "Tropheryma"
#> [479] "Trueperella"
#> [480] "Turicibacter"
#> [481] "Tuzzerella"
#> [482] "Tyzzerella"
#> [483] "UBA1819"
#> [484] "UC5-1-2E3"
#> [485] "UCG-002"
#> [486] "UCG-003"
#> [487] "UCG-004"
#> [488] "UCG-005"
#> [489] "UCG-007"
#> [490] "UCG-008"
#> [491] "UCG-009"
#> [492] "Ureibacillus"
#> [493] "Varibaculum"
#> [494] "Variovorax"
#> [495] "Veillonella"
#> [496] "Verticiella"
#> [497] "Victivallis"
#> [498] "Vulcaniibacterium"
#> [499] "Weissella"
#> [500] "Xanthomonas"
#> [501] "Yersinia"
#> [502] "Yokenella"
#> [503] "Zoogloea"
#> [504] "[Bacteroides] pectinophilus group"
#> [505] "[Clostridium] innocuum group"
#> [506] "[Eubacterium] brachy group"
#> [507] "[Eubacterium] eligens group"
#> [508] "[Eubacterium] fissicatena group"
#> [509] "[Eubacterium] hallii group"
#> [510] "[Eubacterium] nodatum group"
#> [511] "[Eubacterium] oxidoreducens group"
#> [512] "[Eubacterium] ruminantium group"
#> [513] "[Eubacterium] siraeum group"
#> [514] "[Eubacterium] ventriosum group"
#> [515] "[Eubacterium] xylanophilum group"
#> [516] "[Ruminococcus] gauvreauii group"
#> [517] "[Ruminococcus] gnavus group"
#> [518] "[Ruminococcus] torques group"
#> [519] "unclassified 0319-6G20"
#> [520] "unclassified 67-14"
#> [521] "unclassified A0839"
#> [522] "unclassified Acetobacteraceae"
#> [523] "unclassified Acidaminococcaceae"
#> [524] "unclassified Actinobacteria"
#> [525] "unclassified Actinomycetaceae"
#> [526] "unclassified Aeromonadales"
#> [527] "unclassified Anaerococcus"
#> [528] "unclassified Anaerosalibacter"
#> [529] "unclassified Anaerovoracaceae"
#> [530] "unclassified Armatimonadales"
#> [531] "unclassified Atopobiaceae"
#> [532] "unclassified Bacillaceae"
#> [533] "unclassified Bacillales"
#> [534] "unclassified Bacilli"
#> [535] "unclassified Bacteroidales"
#> [536] "unclassified Bacteroidia"
#> [537] "unclassified Barnesiellaceae"
#> [538] "unclassified Bifidobacteriaceae"
#> [539] "unclassified Burkholderiales"
#> [540] "unclassified Butyricicoccaceae"
#> [541] "unclassified Caloramatoraceae"
#> [542] "unclassified Carnobacteriaceae"
#> [543] "unclassified Caulobacteraceae"
#> [544] "unclassified Chloroplast"
#> [545] "unclassified Christensenellaceae"
#> [546] "unclassified Chroococcidiopsaceae"
#> [547] "unclassified Clostridia UCG-014"
#> [548] "unclassified Clostridia"
#> [549] "unclassified Clostridia vadinBB60 group"
#> [550] "unclassified Clostridiaceae"
#> [551] "unclassified Clostridiales"
#> [552] "unclassified Comamonadaceae"
#> [553] "unclassified Coriobacteriales Incertae Sedis [EUPATH_0009256_Bacteria_Actinobacteriota_Coriobacteriia_Coriobacteriales_Coriobacteriales_Incertae_Sedis_]"
#> [554] "unclassified Coriobacteriales"
#> [555] "unclassified Corynebacteriaceae"
#> [556] "unclassified Desulfovibrionaceae"
#> [557] "unclassified Devosiaceae"
#> [558] "unclassified Diplorickettsiaceae"
#> [559] "unclassified Eggerthellaceae"
#> [560] "unclassified Enterobacterales"
#> [561] "unclassified Enterobacteriaceae"
#> [562] "unclassified Enterococcaceae"
#> [563] "unclassified Erwiniaceae"
#> [564] "unclassified Erysipelatoclostridiaceae"
#> [565] "unclassified Erysipelotrichaceae"
#> [566] "unclassified Erysipelotrichales"
#> [567] "unclassified Ethanoligenenaceae"
#> [568] "unclassified Eubacteriaceae"
#> [569] "unclassified Ezakiella"
#> [570] "unclassified Fastidiosipila"
#> [571] "unclassified Fenollaria"
#> [572] "unclassified Fimbriimonadaceae"
#> [573] "unclassified Finegoldia"
#> [574] "unclassified Firmicutes"
#> [575] "unclassified Flavobacteriaceae"
#> [576] "unclassified Flavobacteriales"
#> [577] "unclassified Fusobacteriaceae"
#> [578] "unclassified Gaiellales"
#> [579] "unclassified Gallicola"
#> [580] "unclassified Gammaproteobacteria"
#> [581] "unclassified Gastranaerophilales"
#> [582] "unclassified Gemmataceae"
#> [583] "unclassified Hungateiclostridiaceae"
#> [584] "unclassified Hydrogenoanaerobacterium"
#> [585] "unclassified Izemoplasmatales"
#> [586] "unclassified JI49D030"
#> [587] "unclassified KD3-93"
#> [588] "unclassified Kapabacteriales"
#> [589] "unclassified Lachnospiraceae"
#> [590] "unclassified Lachnospirales"
#> [591] "unclassified Lactobacillales"
#> [592] "unclassified Leuconostocaceae"
#> [593] "unclassified Lineage IV"
#> [594] "unclassified MAT-CR-H4-C10"
#> [595] "unclassified Methylococcaceae"
#> [596] "unclassified Micavibrionales"
#> [597] "unclassified Microbacteriaceae"
#> [598] "unclassified Micrococcaceae"
#> [599] "unclassified Micrococcales"
#> [600] "unclassified Mitochondria"
#> [601] "unclassified Moraxellaceae"
#> [602] "unclassified Murdochiella"
#> [603] "unclassified Muribaculaceae"
#> [604] "unclassified NS9 marine group"
#> [605] "unclassified Neisseriaceae"
#> [606] "unclassified OLB14"
#> [607] "unclassified Opitutales"
#> [608] "unclassified Oscillospiraceae"
#> [609] "unclassified Oscillospirales"
#> [610] "unclassified Oxalobacteraceae"
#> [611] "unclassified P5D1-392"
#> [612] "unclassified PLTA13"
#> [613] "unclassified Paenibacillaceae"
#> [614] "unclassified Paracaedibacteraceae"
#> [615] "unclassified Parachlamydiaceae"
#> [616] "unclassified Parvimonas"
#> [617] "unclassified Pasteurellaceae"
#> [618] "unclassified Peptococcaceae"
#> [619] "unclassified Peptoniphilus"
#> [620] "unclassified Peptostreptococcaceae"
#> [621] "unclassified Peptostreptococcales-Tissierellales"
#> [622] "unclassified Planctomycetales"
#> [623] "unclassified Planococcaceae"
#> [624] "unclassified Prevotellaceae"
#> [625] "unclassified Promicromonosporaceae"
#> [626] "unclassified Propionibacteriaceae"
#> [627] "unclassified Proteobacteria"
#> [628] "unclassified Pseudomonadaceae"
#> [629] "unclassified Puniceicoccaceae"
#> [630] "unclassified RF39"
#> [631] "unclassified Rhizobiaceae"
#> [632] "unclassified Rhizobiales Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Rhizobiales_Incertae_Sedis_]"
#> [633] "unclassified Rhizobiales"
#> [634] "unclassified Rhodobacteraceae"
#> [635] "unclassified Rhodocyclaceae"
#> [636] "unclassified Rhodospirillales"
#> [637] "unclassified Rickettsiales"
#> [638] "unclassified Rikenellaceae"
#> [639] "unclassified Ruminiclostridium"
#> [640] "unclassified Ruminococcaceae"
#> [641] "unclassified ST-12K33"
#> [642] "unclassified Saccharimonadales"
#> [643] "unclassified Sandaracinaceae"
#> [644] "unclassified Selenomonadaceae"
#> [645] "unclassified Simkaniaceae"
#> [646] "unclassified Solimonadaceae"
#> [647] "unclassified Sphingobacteriales"
#> [648] "unclassified Sphingomonadaceae"
#> [649] "unclassified Staphylococcaceae"
#> [650] "unclassified Streptococcaceae"
#> [651] "unclassified Succinivibrionaceae"
#> [652] "unclassified Sutterellaceae"
#> [653] "unclassified TRA3-20"
#> [654] "unclassified Tannerellaceae"
#> [655] "unclassified Tepidimicrobium"
#> [656] "unclassified UCG-010"
#> [657] "unclassified UCG-011"
#> [658] "unclassified Veillonellaceae"
#> [659] "unclassified Veillonellales-Selenomonadales"
#> [660] "unclassified Vermiphilaceae"
#> [661] "unclassified Verrucomicrobiales"
#> [662] "unclassified Verrucomicrobiota"
#> [663] "unclassified Victivallaceae"
#> [664] "unclassified W5053"
#> [665] "unclassified WPS-2"
#> [666] "unclassified Weeksellaceae"
#> [667] "unclassified Xanthobacteraceae"
#> [668] "unclassified Yersiniaceae"
#> [669] "unclassified [Clostridium] methylpentosum group"
#> [670] "unclassified [Eubacterium] coprostanoligenes group"
#> [671] "unclassified vadinBE97"
getMetadataVariableNames(microbiomeData::DiabImmune)
#> [1] "Participant_Id"
#> [2] "participant_repeated_measure_Id"
#> [3] "age_months"
#> [4] "age_1st_animal_milk_or_solids_given_days"
#> [5] "age_1st_given_apple_months"
#> [6] "age_1st_given_banana_months"
#> [7] "age_1st_given_barley_months"
#> [8] "age_1st_given_beef_months"
#> [9] "age_1st_given_berries_months"
#> [10] "age_1st_given_cabbs_months"
#> [11] "age_1st_given_carrot_months"
#> [12] "age_1st_given_corn_months"
#> [13] "age_1st_given_cowsmilk_months"
#> [14] "age_1st_given_egg_months"
#> [15] "age_1st_given_fish_months"
#> [16] "age_1st_given_milk_products_months"
#> [17] "age_1st_given_oat_months"
#> [18] "age_1st_given_pear_months"
#> [19] "age_1st_given_peas_months"
#> [20] "age_1st_given_plum_months"
#> [21] "age_1st_given_pork_months"
#> [22] "age_1st_given_potato_months"
#> [23] "age_1st_given_poultry_months"
#> [24] "age_1st_given_rice_months"
#> [25] "age_1st_given_rye_months"
#> [26] "age_1st_given_sweet_potato_months"
#> [27] "age_1st_given_tomato_months"
#> [28] "age_1st_given_wheat_months"
#> [29] "age_at_anthropometry_days"
#> [30] "age_at_two_autoantibodies_positive_days"
#> [31] "age_at_type_1_diabetes_diagnosis_days"
#> [32] "antibiotics_before_delivery_by_maternal_report"
#> [33] "bmi_minus_for_minus_age_z_minus_score"
#> [34] "breastfed_duration"
#> [35] "country"
#> [36] "delivery_mode"
#> [37] "diet_in_first_three_days"
#> [38] "exclusive_breastfed_duration"
#> [39] "gestational_diabetes_by_maternal_report"
#> [40] "glutamic_acid_decarboxylase_antibodies"
#> [41] "hla_risk_by_hla_haplotyping"
#> [42] "height_minus_for_minus_age_z_minus_score"
#> [43] "insulin_autoantibodies"
#> [44] "insulinoma_minus_associated_protein_2_autoantibodies"
#> [45] "islet_cell_autoantibodies"
#> [46] "linear_growth_during_1st_year_cm"
#> [47] "maternal_age_at_birth_year"
#> [48] "mean_linear_growth_during_1st_3_years_cm_year"
#> [49] "mean_weight_gain_during_1st_3_years_kg_year"
#> [50] "sex"
#> [51] "study_group"
#> [52] "type_1_diabetes_diagnosed"
#> [53] "urban_or_rural_site"
#> [54] "weight_gain_during_1st_year_kg"
#> [55] "weight_minus_for_minus_age_z_minus_score"
#> [56] "zinc_transporter_8_autoantibodies"
#> [57] "Sample_Id"
#> [58] "habitat"
#> [59] "host_body_habitat"
#> [60] "host_body_product"
#> [61] "host_body_site"
#> [62] "sample_type"
variablesDT <- getVariables(
microbiomeData::DiabImmune,
list("metadata" = c("age_months", "sex"),
"16S (V4) Genus (Relative taxonomic abundance analysis)" = "Bacteroides",
"Shotgun metagenomics Metagenome enzyme pathway abundance data" = "ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)"
)
)
#>
#> 2024-06-26 14:28:49.62304 Removed 300 records with no data.