Function reference • MicrobiomeDB

All functions

DESeqDataSetFromCollection(): DESeqDataSet object from a Collection

Maaslin2(): Maaslin2 from a Collection

MbioDataset-class: MicrobiomeDB Dataset

MbioDataset(): Create a Microbiome Dataset

alphaDiv(): Alpha diversity

betaDiv(): Beta diversity

correlation(): Correlation

correlationNetwork(): Correlation Network Visualization

differentialAbundance(): Differential abundance

getCollection(): Get Microbiome Dataset Collection

getCollectionNames(<MbioDataset>): Get Names of Collections

getCollectionVariableNames(<MbioDataset>): Get Microbiome Dataset Collection Variable Names

getComputeResult(): Get Microbiome Dataset Compute Result

getComputeResultWithMetadata(): Get Microbiome Dataset Compute Result With Metadata

getMetadataVariableNames(<MbioDataset>): Get Variable Names of Metadata

getMetadataVariableSummary(<MbioDataset>): Get Summary of Metadata Variables

getSampleMetadata(<MbioDataset>): Get data.table of sample metadata from MbioDataset

getSampleMetadataIdColumns(<MbioDataset>): Get Sample Metadata Id Column Names

getVariables(): Get Microbiome Dataset Variables

importBIOM(): Import BIOM data

importDADA2(): Import DADA2 data

importHUMAnN(): Import HUMAnN data

importMetaPhlAn(): Import MetaPhlAn data

importMothur(): Import MOTHUR data

importPhyloseq(): Import Phyloseq data

importQIIME2(): Import QIIME2 data

importTreeSummarizedExperiment() importTreeSE(): Import TreeSummarizedExperiment

rankedAbundance(): Ranked abundance

selfCorrelation(): Self Correlation

updateCollectionName(): Update Microbiome Dataset Collection Name