# Microbiome analysis

## Documentation for package ‘mia’ version 1.12.0

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

## Help Pages

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

mia-package | 'mia' Package.

## -- A --

addCluster | Clustering wrapper
addCluster-method | Clustering wrapper
addContaminantQC | decontam functions
addContaminantQC-method | decontam functions
addDivergence | Estimate divergence
addDivergence-method | Estimate divergence
addHierarchyTree | Calculate hierarchy tree
addHierarchyTree-method | Calculate hierarchy tree
addNotContaminantQC | decontam functions
addNotContaminantQC-method | decontam functions
addPerSampleDominantFeatures | Get dominant taxa
addPerSampleDominantFeatures-method | Get dominant taxa
addPerSampleDominantTaxa | Get dominant taxa
addPerSampleDominantTaxa-method | Get dominant taxa
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
agglomerateByPrevalence | Agglomerate data using taxonomic information
agglomerateByPrevalence-method | Agglomerate data using taxonomic information
agglomerateByRank | Agglomerate data using taxonomic information
agglomerateByRank-method | Agglomerate data using taxonomic information

## -- 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
calculateCCA-method | 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 Correspondance analysis
calculateDPCoA-method | Calculation of Double Principal Correspondance analysis
calculateJSD | Calculate the Jensen-Shannon Divergence
calculateJSD-method | Calculate the Jensen-Shannon Divergence
calculateNMDS | Perform non-metric MDS on sample-level data
calculateNMDS-method | Perform non-metric MDS on sample-level data
calculateOverlap | Estimate overlap
calculateOverlap-method | Estimate overlap
calculateRDA | Canonical Correspondence Analysis and Redundancy Analysis
calculateRDA-method | Canonical Correspondence Analysis and Redundancy Analysis
calculateUnifrac | Calculate weighted or unweighted (Fast) Unifrac distance
calculateUnifrac-method | Calculate weighted or unweighted (Fast) Unifrac distance
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.
countDominantFeatures | Summarizing microbiome data
countDominantFeatures-method | Summarizing microbiome data
countDominantTaxa | Summarizing microbiome data
countDominantTaxa-method | Summarizing microbiome data

## -- D --

deprecate | These functions will be deprecated. Please use other functions instead.
dmn_se | dmn_se

## -- E --

enterotype | enterotype
esophagus | esophagus
estimateDivergence | These functions will be deprecated. Please use other functions instead.
estimateDivergence-method | These functions will be deprecated. Please use other functions instead.
estimateDiversity | Estimate (alpha) diversity measures
estimateDiversity-method | Estimate (alpha) diversity measures
estimateDominance | Estimate dominance measures
estimateDominance-method | Estimate dominance measures
estimateEvenness | Estimate Evenness measures
estimateEvenness-method | Estimate Evenness measures
estimateFaith | Estimate (alpha) diversity measures
estimateFaith-method | Estimate (alpha) diversity measures
estimateRichness | Estimate richness measures
estimateRichness-method | Estimate richness measures

## -- 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 --

getBestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getBestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
getExperimentCrossAssociation | Calculate correlations between features of two experiments.
getExperimentCrossAssociation-method | Calculate correlations between features of two experiments.
getExperimentCrossCorrelation | Calculate correlations between features of two experiments.
getExperimentCrossCorrelation-method | Calculate correlations between features of two experiments.
getHierarchyTree | Calculate hierarchy tree
getHierarchyTree-method | Calculate hierarchy tree
getPrevalence | Calculation prevalence information for features across samples
getPrevalence-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 | Calculation prevalence information for features across samples
getPrevalentFeatures-method | Calculation prevalence information for features across samples
getPrevalentTaxa | Calculation prevalence information for features across samples
getPrevalentTaxa-method | Calculation prevalence information for features across samples
getRareFeatures | Calculation prevalence information for features across samples
getRareFeatures-method | Calculation prevalence information for features across samples
getRarePrevalentTaxa | Calculation prevalence information for features across samples
getRareTaxa | Calculation prevalence information for features across samples
getRareTaxa-method | Calculation prevalence information for features across samples
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'.
getTopFeatures | Summarizing microbiome data
getTopFeatures-method | Summarizing microbiome data
getTopTaxa | Summarizing microbiome data
getTopTaxa-method | Summarizing microbiome data
getUniqueFeatures | Summarizing microbiome data
getUniqueFeatures-method | Summarizing microbiome data
getUniqueTaxa | Summarizing microbiome data
getUniqueTaxa-method | Summarizing microbiome data
GlobalPatterns | GlobalPatterns

## -- H --

hierarchy-tree | Calculate hierarchy tree
HintikkaXOData | HintikkaXOData

## -- I --

IdTaxaToDataFrame | Functions for accessing taxonomic data stored in 'rowData'.
importBIOM | Loading a biom file
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'
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 | Create a phyloseq object from a TreeSummarizedExperiment object
makePhyloseqFromTreeSE-method | Create a phyloseq object from a TreeSummarizedExperiment object
makePhyloseqFromTreeSummarizedExperiment | Create a phyloseq object from a TreeSummarizedExperiment object
makePhyloseqFromTreeSummarizedExperiment-method | Create a phyloseq object from a TreeSummarizedExperiment object
makeTreeSEFromBiom | Loading a biom file
makeTreeSEFromDADA2 | Coerce 'DADA2' results to 'TreeSummarizedExperiment'
makeTreeSEFromPhyloseq | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment'
makeTreeSummarizedExperimentFromBiom | Loading a biom file
makeTreeSummarizedExperimentFromDADA2 | Coerce 'DADA2' results to 'TreeSummarizedExperiment'
makeTreeSummarizedExperimentFromPhyloseq | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment'
makeTreeSummarizedExperimentFromPhyloseq-method | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment'
mapTaxonomy | Functions for accessing taxonomic data stored in 'rowData'.
mapTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'.
meltAssay | Converting a 'SummarizedExperiment' object into a long data.frame
meltAssay-method | Converting a 'SummarizedExperiment' object into a long data.frame
merge-methods | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeCols | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeCols-method | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeFeatures | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeFeatures-method | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeFeaturesByPrevalence | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByPrevalence-method | These functions will be deprecated. Please use other functions instead.
mergeFeaturesByRank | Agglomerate data using taxonomic information
mergeFeaturesByRank-method | Agglomerate data using taxonomic information
mergeRows | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeRows-method | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeSamples | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeSamples-method | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mergeSEs | Merge SE objects into single SE object.
mergeSEs-method | Merge SE objects into single SE object.
mergeSmaples | Merge a subset of the rows or columns of a 'SummarizedExperiment'
mia | 'mia' Package.
mia-datasets | mia datasets

## -- P --

peerj13075 | peerj13075
performDMNgroupCV | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
performDMNgroupCV-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
perSampleDominantFeatures | Get dominant taxa
perSampleDominantFeatures-method | Get dominant taxa
perSampleDominantTaxa | Get dominant taxa
perSampleDominantTaxa-method | Get dominant taxa
plotNMDS | These functions will be deprecated. Please use other functions instead.

## -- R --

rarifyCounts | Subsample Counts
readQZA | These functions will be deprecated. Please use other functions instead.
relabundance | Getter / setter for relative abundance data
relabundance-method | Getter / setter for relative abundance data
relabundance<- | Getter / setter for relative abundance data
relabundance<--method | Getter / setter for relative abundance data
relAbundanceCounts | Transform assay
relAbundanceCounts-method | Transform assay
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
runCCA-method | Canonical Correspondence Analysis and Redundancy Analysis
runDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
runDPCoA | Calculation of Double Principal Correspondance analysis
runJSD | Calculate the Jensen-Shannon Divergence
runNMDS | Perform non-metric MDS on sample-level data
runOverlap | Estimate overlap
runOverlap-method | Estimate overlap
runRDA | Canonical Correspondence Analysis and Redundancy Analysis
runRDA-method | Canonical Correspondence Analysis and Redundancy Analysis
runUnifrac | Calculate weighted or unweighted (Fast) Unifrac distance

## -- S --

setTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'.
splitByRanks | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks
splitByRanks-method | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks
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 | Subsample Counts
subsampleCounts-method | Subsample Counts
subsetByPrevalentFeatures | Calculation prevalence information for features across samples
subsetByPrevalentFeatures-method | Calculation prevalence information for features across samples
subsetByPrevalentTaxa | Calculation prevalence information for features across samples
subsetByPrevalentTaxa-method | Calculation prevalence information for features across samples
subsetByRareFeatures | Calculation prevalence information for features across samples
subsetByRareFeatures-method | Calculation prevalence information for features across samples
subsetByRareTaxa | Calculation prevalence information for features across samples
subsetByRareTaxa-method | Calculation prevalence information for features across samples
subsetFeatures | Subset functions
subsetFeatures-method | Subset functions
subsetSamples | Subset functions
subsetSamples-method | Subset functions
subsetTaxa | Subset functions
subsetTaxa-method | Subset functions
summaries | 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.
TAXONOMY_RANKS | Functions for accessing taxonomic data stored in 'rowData'.
Tengeler2020 | Tengeler2020
testExperimentCrossAssociation | Calculate correlations between features of two experiments.
testExperimentCrossAssociation-method | Calculate correlations between features of two experiments.
testExperimentCrossCorrelation | Calculate correlations between features of two experiments.
testExperimentCrossCorrelation-method | Calculate correlations between features of two experiments.
transformAssay | Transform assay
transformAssay-method | Transform assay
transformCounts | Transform assay
transformFeatures | Transform assay
transformFeatures-method | Transform assay
transformSamples | Transform assay
transformSamples-method | Transform assay
twins | dmn_se

## -- U --

unsplitByRanks | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks
unsplitByRanks-method | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks
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

## -- Z --

ZTransform | Transform assay
ZTransform-method | Transform assay