# Microbiome analysis

## Documentation for package ‘mia’ version 1.21.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M P R S T U Z

mia-package | 'mia' Package.

## -- A --

addAbundanceClass | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
addAbundanceClass-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
addAlpha | Estimate alpha diversity indices
addAlpha-method | Estimate alpha diversity indices
addCCA | Canonical Correspondence Analysis and Redundancy Analysis
addCCA-method | Canonical Correspondence Analysis and Redundancy Analysis
addCluster | Clustering wrapper
addCluster-method | Clustering wrapper
addContaminantQC | decontam functions
addContaminantQC-method | decontam functions
addDissimilarity | Calculate dissimilarities
addDissimilarity-method | Calculate dissimilarities
addDivergence | Estimate divergence
addDivergence-method | Estimate divergence
addDominant | Get dominant taxa
addDominant-method | Get dominant taxa
addDPCoA | Calculation of Double Principal Correspondence analysis
addHierarchyTree | Calculate hierarchy tree
addHierarchyTree-method | Calculate hierarchy tree
addJointRPCA | Run (joint) robust principal component analysis (RPCA)
addJointRPCA-method | Run (joint) robust principal component analysis (RPCA)
addLDA | Latent Dirichlet Allocation
addLDA-method | Latent Dirichlet Allocation
addMDS | Perform multi-dimensional scaling (MDS)
addMDS-method | Perform multi-dimensional scaling (MDS)
addMediation | Perform mediation analysis
addMediation-method | Perform mediation analysis
addNMDS | Perform non-metric MDS on sample-level data
addNMF | Non-negative Matrix Factorization
addNMF-method | Non-negative Matrix Factorization
addNotContaminantQC | decontam functions
addNotContaminantQC-method | decontam functions
addPERMANOVA | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)
addPERMANOVA-method | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)
addPerSampleDominantFeatures | These functions will be deprecated. Please use other functions instead.
addPerSampleDominantFeatures-method | These functions will be deprecated. Please use other functions instead.
addPerSampleDominantTaxa | These functions will be deprecated. Please use other functions instead.
addPerSampleDominantTaxa-method | These functions will be deprecated. Please use other functions instead.
addPrevalence | Calculation prevalence information for features across samples
addPrevalence-method | Calculation prevalence information for features across samples
addPrevalentAbundance | Calculation prevalence information for features across samples
addPrevalentAbundance-method | Calculation prevalence information for features across samples
addRDA | Canonical Correspondence Analysis and Redundancy Analysis
addRDA-method | Canonical Correspondence Analysis and Redundancy Analysis
addRPCA | Run (joint) robust principal component analysis (RPCA)
addRPCA-method | Run (joint) robust principal component analysis (RPCA)
addTaxonomyTree | These functions will be deprecated. Please use other functions instead.
addTaxonomyTree-method | These functions will be deprecated. Please use other functions instead.
agglomerate-methods | Agglomerate data using taxonomic information or other grouping
agglomerateByModule | Agglomerate data using taxonomic information or other grouping
agglomerateByModule-method | Agglomerate data using taxonomic information or other grouping
agglomerateByPrevalence | Agglomerate data based on population prevalence
agglomerateByPrevalence-method | Agglomerate data based on population prevalence
agglomerateByRank | Agglomerate data using taxonomic information or other grouping
agglomerateByRank-method | Agglomerate data using taxonomic information or other grouping
agglomerateByRanks | Agglomerate data using taxonomic information or other grouping
agglomerateByRanks-method | Agglomerate data using taxonomic information or other grouping
agglomerateByVariable | Agglomerate data using taxonomic information or other grouping
agglomerateByVariable-method | Agglomerate data using taxonomic information or other grouping

## -- B --

bestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
bestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data

## -- C --

calculateCCA | Canonical Correspondence Analysis and Redundancy Analysis
calculateDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
calculateDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
calculateDMNgroup | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
calculateDMNgroup-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
calculateDPCoA | Calculation of Double Principal Correspondence analysis
calculateJSD | These functions will be deprecated. Please use other functions instead.
calculateJSD-method | These functions will be deprecated. Please use other functions instead.
calculateNMDS | Perform non-metric MDS on sample-level data
calculateOverlap | These functions will be deprecated. Please use other functions instead.
calculateOverlap-method | These functions will be deprecated. Please use other functions instead.
calculateRDA | Canonical Correspondence Analysis and Redundancy Analysis
calculateUnifrac | These functions will be deprecated. Please use other functions instead.
calculateUnifrac-method | These functions will be deprecated. Please use other functions instead.
checkTaxonomy | Functions for accessing taxonomic data stored in 'rowData'.
checkTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'.
cluster | These functions will be deprecated. Please use other functions instead.
cluster-method | These functions will be deprecated. Please use other functions instead.
convertFromBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results
convertFromDADA2 | Create a 'TreeSummarizedExperiment' object from 'DADA2' results
convertFromPhyloseq | Create a 'TreeSummarizedExperiment' object from a phyloseq object
convertToBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results
convertToBIOM-method | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results
convertToPhyloseq | Create a 'TreeSummarizedExperiment' object from a phyloseq object
convertToPhyloseq-method | Create a 'TreeSummarizedExperiment' object from a phyloseq object
countDominantFeatures | These functions will be deprecated. Please use other functions instead.
countDominantFeatures-method | These functions will be deprecated. Please use other functions instead.
countDominantTaxa | These functions will be deprecated. Please use other functions instead.
countDominantTaxa-method | These functions will be deprecated. Please use other functions instead.

## -- D --

deprecate | These functions will be deprecated. Please use other functions instead.
dmn_se | Twins' microbiome data from 278 individuals

## -- E --

enterotype | Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing
esophagus | Human esophageal community from 3 individuals
estimateDivergence | These functions will be deprecated. Please use other functions instead.
estimateDivergence-method | These functions will be deprecated. Please use other functions instead.
estimateDiversity | These functions will be deprecated. Please use other functions instead.
estimateDiversity-method | These functions will be deprecated. Please use other functions instead.
estimateDominance | These functions will be deprecated. Please use other functions instead.
estimateDominance-method | These functions will be deprecated. Please use other functions instead.
estimateEvenness | These functions will be deprecated. Please use other functions instead.
estimateEvenness-method | These functions will be deprecated. Please use other functions instead.
estimateFaith | These functions will be deprecated. Please use other functions instead.
estimateFaith-method | These functions will be deprecated. Please use other functions instead.
estimateRichness | These functions will be deprecated. Please use other functions instead.
estimateRichness-method | These functions will be deprecated. Please use other functions instead.

## -- F --

full_join | These functions will be deprecated. Please use other functions instead.
full_join-method | These functions will be deprecated. Please use other functions instead.

## -- G --

getAbundanceClass | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getAbundanceClass-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getAlpha | Estimate alpha diversity indices
getAlpha-method | Estimate alpha diversity indices
getBestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getBestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getCCA | Canonical Correspondence Analysis and Redundancy Analysis
getCCA-method | Canonical Correspondence Analysis and Redundancy Analysis
getCluster | Clustering wrapper
getCluster-method | Clustering wrapper
getConditionallyLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getConditionallyLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getCrossAssociation | Calculate correlations between features of two experiments.
getCrossAssociation-method | Calculate correlations between features of two experiments.
getDissimilarity | Calculate dissimilarities
getDissimilarity-method | Calculate dissimilarities
getDivergence | Estimate divergence
getDivergence-method | Estimate divergence
getDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getDominant | Get dominant taxa
getDominant-method | Get dominant taxa
getDPCoA | Calculation of Double Principal Correspondence analysis
getDPCoA-method | Calculation of Double Principal Correspondence analysis
getExperimentCrossAssociation | These functions will be deprecated. Please use other functions instead.
getExperimentCrossAssociation-method | These functions will be deprecated. Please use other functions instead.
getExperimentCrossCorrelation | These functions will be deprecated. Please use other functions instead.
getExperimentCrossCorrelation-method | These functions will be deprecated. Please use other functions instead.
getHierarchyTree | Calculate hierarchy tree
getHierarchyTree-method | Calculate hierarchy tree
getJointRPCA | Run (joint) robust principal component analysis (RPCA)
getJointRPCA-method | Run (joint) robust principal component analysis (RPCA)
getLDA | Latent Dirichlet Allocation
getLDA-method | Latent Dirichlet Allocation
getLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getMDS | Perform multi-dimensional scaling (MDS)
getMDS-method | Perform multi-dimensional scaling (MDS)
getMediation | Perform mediation analysis
getMediation-method | Perform mediation analysis
getNMDS | Perform non-metric MDS on sample-level data
getNMDS-method | Perform non-metric MDS on sample-level data
getNMF | Non-negative Matrix Factorization
getNMF-method | Non-negative Matrix Factorization
getPermanentlyLowAbundant | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getPermanentlyLowAbundant-method | Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.
getPERMANOVA | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)
getPERMANOVA-method | Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)
getPrevalence | Calculation prevalence information for features across samples
getPrevalence-method | Calculation prevalence information for features across samples
getPrevalent | Calculation prevalence information for features across samples
getPrevalent-method | Calculation prevalence information for features across samples
getPrevalentAbundance | Calculation prevalence information for features across samples
getPrevalentAbundance-method | Calculation prevalence information for features across samples
getPrevalentFeatures | These functions will be deprecated. Please use other functions instead.
getPrevalentFeatures-method | These functions will be deprecated. Please use other functions instead.
getPrevalentTaxa | These functions will be deprecated. Please use other functions instead.
getPrevalentTaxa-method | These functions will be deprecated. Please use other functions instead.
getRare | Calculation prevalence information for features across samples
getRare-method | Calculation prevalence information for features across samples
getRareFeatures | These functions will be deprecated. Please use other functions instead.
getRareFeatures-method | These functions will be deprecated. Please use other functions instead.
getRareTaxa | These functions will be deprecated. Please use other functions instead.
getRareTaxa-method | These functions will be deprecated. Please use other functions instead.
getRDA | Canonical Correspondence Analysis and Redundancy Analysis
getRDA-method | Canonical Correspondence Analysis and Redundancy Analysis
getReducedDimAttribute | Utilization functions for 'TreeSummarizedExperiment' objects
getReducedDimAttribute-method | Utilization functions for 'TreeSummarizedExperiment' objects
getRPCA | Run (joint) robust principal component analysis (RPCA)
getRPCA-method | Run (joint) robust principal component analysis (RPCA)
getTaxonomyLabels | Functions for accessing taxonomic data stored in 'rowData'.
getTaxonomyLabels-method | Functions for accessing taxonomic data stored in 'rowData'.
getTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'.
getTop | Summarizing microbiome data
getTop-method | Summarizing microbiome data
getTopFeatures | These functions will be deprecated. Please use other functions instead.
getTopFeatures-method | These functions will be deprecated. Please use other functions instead.
getTopTaxa | These functions will be deprecated. Please use other functions instead.
getTopTaxa-method | These functions will be deprecated. Please use other functions instead.
getUnique | Summarizing microbiome data
getUnique-method | Summarizing microbiome data
getUniqueFeatures | These functions will be deprecated. Please use other functions instead.
getUniqueFeatures-method | These functions will be deprecated. Please use other functions instead.
getUniqueTaxa | These functions will be deprecated. Please use other functions instead.
getUniqueTaxa-method | These functions will be deprecated. Please use other functions instead.
GlobalPatterns | Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

## -- H --

hierarchy-tree | Calculate hierarchy tree
HintikkaXOData | Multiomics dataset from 40 rat samples

## -- I --

ibdmdb | IBDMDB 2-omic demo dataset (MGX + MTX)
IdTaxaToDataFrame | Functions for accessing taxonomic data stored in 'rowData'.
importBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results
importHUMAnN | Import HUMAnN results to 'TreeSummarizedExperiment'
importMetaPhlAn | Import Metaphlan results to 'TreeSummarizedExperiment'
importMothur | Import Mothur results as a 'TreeSummarizedExperiment'
importQIIME2 | Import QIIME2 results to 'TreeSummarizedExperiment'
importQZA | Import QIIME2 results to 'TreeSummarizedExperiment'
importTaxpasta | Import taxpasta-specific BIOM results to 'TreeSummarizedExperiment'
inner_join | These functions will be deprecated. Please use other functions instead.
inner_join-method | These functions will be deprecated. Please use other functions instead.
isContaminant | decontam functions
isContaminant-method | decontam functions
isNotContaminant-method | decontam functions

## -- L --

left_join | These functions will be deprecated. Please use other functions instead.
left_join-method | These functions will be deprecated. Please use other functions instead.
loadFromBiom | These functions will be deprecated. Please use other functions instead.
loadFromHumann | These functions will be deprecated. Please use other functions instead.
loadFromMetaphlan | These functions will be deprecated. Please use other functions instead.
loadFromMothur | These functions will be deprecated. Please use other functions instead.
loadFromQIIME2 | These functions will be deprecated. Please use other functions instead.

## -- M --

makePhyloseqFromTreeSE | These functions will be deprecated. Please use other functions instead.
makePhyloseqFromTreeSE-method | These functions will be deprecated. Please use other functions instead.
makePhyloseqFromTreeSummarizedExperiment | These functions will be deprecated. Please use other functions instead.
makePhyloseqFromTreeSummarizedExperiment-method | These functions will be deprecated. Please use other functions instead.
makeTreeSEFromBiom | These functions will be deprecated. Please use other functions instead.
makeTreeSEFromDADA2 | These functions will be deprecated. Please use other functions instead.
makeTreeSEFromPhyloseq | These functions will be deprecated. Please use other functions instead.
makeTreeSummarizedExperimentFromBiom | These functions will be deprecated. Please use other functions instead.
makeTreeSummarizedExperimentFromDADA2 | These functions will be deprecated. Please use other functions instead.
makeTreeSummarizedExperimentFromPhyloseq | These functions will be deprecated. Please use other functions instead.
makeTreeSummarizedExperimentFromPhyloseq-method | These functions will be deprecated. Please use other functions instead.
mapTaxonomy | Functions for accessing taxonomic data stored in 'rowData'.
mapTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'.
meltAssay | These functions will be deprecated. Please use other functions instead.
meltAssay-method | These functions will be deprecated. Please use other functions instead.
meltSE | Converting a 'SummarizedExperiment' object into a long data.frame
meltSE-method | Converting a 'SummarizedExperiment' object into a long data.frame
mergeCols | These functions will be deprecated. Please use other functions instead.
mergeCols-method | These functions will be deprecated. Please use other functions instead.
mergeFeatures | These functions will be deprecated. Please use other functions instead.
mergeFeatures-method | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByPrevalence | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByPrevalence-method | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByRank | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByRank-method | These functions will be deprecated. Please use other functions instead.
mergeRows | These functions will be deprecated. Please use other functions instead.
mergeRows-method | These functions will be deprecated. Please use other functions instead.
mergeSamples | These functions will be deprecated. Please use other functions instead.
mergeSamples-method | These functions will be deprecated. Please use other functions instead.
mergeSEs | Merge SE objects into single SE object.
mergeSEs-method | Merge SE objects into single SE object.
mia | 'mia' Package.
mia-datasets | mia datasets

## -- P --

peerj13075 | Skin microbial profiles 58 genetically unrelated individuals
performDMNgroupCV | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
performDMNgroupCV-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
perSampleDominantFeatures | These functions will be deprecated. Please use other functions instead.
perSampleDominantFeatures-method | These functions will be deprecated. Please use other functions instead.
perSampleDominantTaxa | These functions will be deprecated. Please use other functions instead.
perSampleDominantTaxa-method | These functions will be deprecated. Please use other functions instead.
plotNMDS | These functions will be deprecated. Please use other functions instead.

## -- R --

rarefyAssay | Subsample Counts
rarefyAssay-method | Subsample Counts
readQZA | These functions will be deprecated. Please use other functions instead.
relabundance | These functions will be deprecated. Please use other functions instead.
relabundance-method | These functions will be deprecated. Please use other functions instead.
relabundance<- | These functions will be deprecated. Please use other functions instead.
relabundance<--method | These functions will be deprecated. Please use other functions instead.
relAbundanceCounts | These functions will be deprecated. Please use other functions instead.
relAbundanceCounts-method | These functions will be deprecated. Please use other functions instead.
right_join | These functions will be deprecated. Please use other functions instead.
right_join-method | These functions will be deprecated. Please use other functions instead.
runCCA | Canonical Correspondence Analysis and Redundancy Analysis
runDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
runDPCoA | Calculation of Double Principal Correspondence analysis
runJSD | These functions will be deprecated. Please use other functions instead.
runJSD-method | These functions will be deprecated. Please use other functions instead.
runNMDS | Perform non-metric MDS on sample-level data
runOverlap | These functions will be deprecated. Please use other functions instead.
runOverlap-method | These functions will be deprecated. Please use other functions instead.
runRDA | Canonical Correspondence Analysis and Redundancy Analysis
runUnifrac | These functions will be deprecated. Please use other functions instead.

## -- S --

setTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'.
splitByRanks | Agglomerate data using taxonomic information or other grouping
splitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable
splitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable
subsampleCounts | These functions will be deprecated. Please use other functions instead.
subsampleCounts-method | These functions will be deprecated. Please use other functions instead.
subsetByPrevalent | Calculation prevalence information for features across samples
subsetByPrevalent-method | Calculation prevalence information for features across samples
subsetByPrevalentFeatures | These functions will be deprecated. Please use other functions instead.
subsetByPrevalentFeatures-method | These functions will be deprecated. Please use other functions instead.
subsetByPrevalentTaxa | These functions will be deprecated. Please use other functions instead.
subsetByPrevalentTaxa-method | These functions will be deprecated. Please use other functions instead.
subsetByRare | Calculation prevalence information for features across samples
subsetByRare-method | Calculation prevalence information for features across samples
subsetByRareFeatures | These functions will be deprecated. Please use other functions instead.
subsetByRareFeatures-method | These functions will be deprecated. Please use other functions instead.
subsetByRareTaxa | These functions will be deprecated. Please use other functions instead.
subsetByRareTaxa-method | These functions will be deprecated. Please use other functions instead.
subsetFeatures | These functions will be deprecated. Please use other functions instead.
subsetFeatures-method | These functions will be deprecated. Please use other functions instead.
subsetSamples | These functions will be deprecated. Please use other functions instead.
subsetSamples-method | These functions will be deprecated. Please use other functions instead.
subsetTaxa | These functions will be deprecated. Please use other functions instead.
subsetTaxa-method | These functions will be deprecated. Please use other functions instead.
summarizeDominance | Summarizing microbiome data
summarizeDominance-method | Summarizing microbiome data
summary | Summarizing microbiome data
summary-method | Summarizing microbiome data

## -- T --

taxonomy-methods | Functions for accessing taxonomic data stored in 'rowData'.
taxonomyRankEmpty | Functions for accessing taxonomic data stored in 'rowData'.
taxonomyRankEmpty-method | Functions for accessing taxonomic data stored in 'rowData'.
taxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'.
taxonomyRanks-method | Functions for accessing taxonomic data stored in 'rowData'.
taxonomyTree | These functions will be deprecated. Please use other functions instead.
taxonomyTree-method | These functions will be deprecated. Please use other functions instead.
Tengeler2020 | Gut microbiota profiles of 27 individuals with ADHD and healthy controls
testExperimentCrossAssociation | These functions will be deprecated. Please use other functions instead.
testExperimentCrossAssociation-method | These functions will be deprecated. Please use other functions instead.
testExperimentCrossCorrelation | These functions will be deprecated. Please use other functions instead.
testExperimentCrossCorrelation-method | These functions will be deprecated. Please use other functions instead.
Tito2024QMP | Fecal microbiota samples from 589 patients across different colorectal cancer stages
transformAssay | Transform assay
transformAssay-method | Transform assay
transformCounts | These functions will be deprecated. Please use other functions instead.
transformFeatures | These functions will be deprecated. Please use other functions instead.
transformFeatures-method | These functions will be deprecated. Please use other functions instead.
transformSamples | These functions will be deprecated. Please use other functions instead.
transformSamples-method | These functions will be deprecated. Please use other functions instead.
twins | Twins' microbiome data from 278 individuals

## -- U --

unsplitByRanks | Agglomerate data using taxonomic information or other grouping
unsplitByRanks-method | Agglomerate data using taxonomic information or other grouping
unsplitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable
unsplitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable
utilization_functions | Utilization functions for 'TreeSummarizedExperiment' objects

## -- Z --

ZTransform | These functions will be deprecated. Please use other functions instead.
ZTransform-method | These functions will be deprecated. Please use other functions instead.