Microbiome analysis

Documentation for package ‘mia’ version 1.13.23

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'mia' Package.

-- A --

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
addDivergence	Estimate divergence
addDivergence-method	Estimate divergence
addDominant	Get dominant taxa
addDominant-method	Get dominant taxa
addDPCoA	Calculation of Double Principal Correspondance analysis
addHierarchyTree	Calculate hierarchy tree
addHierarchyTree-method	Calculate hierarchy tree
addMediation	Perform mediation analysis
addMediation-method	Perform mediation analysis
addNMDS	Perform non-metric MDS on sample-level data
addNotContaminantQC	decontam functions
addNotContaminantQC-method	decontam functions
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.
addRDA	Canonical Correspondence Analysis and Redundancy Analysis
addRDA-method	Canonical Correspondence Analysis and Redundancy Analysis
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 or merge data using taxonomic information
agglomerateByPrevalence	Agglomerate or merge data using taxonomic information
agglomerateByPrevalence-method	Agglomerate or merge data using taxonomic information
agglomerateByRank	Agglomerate or merge data using taxonomic information
agglomerateByRank-method	Agglomerate or merge data using taxonomic information
agglomerateByRanks	Agglomerate or merge data using taxonomic information
agglomerateByRanks-method	Agglomerate or merge data using taxonomic information
agglomerateByVariable	Agglomerate or merge data using taxonomic information
agglomerateByVariable-method	Agglomerate or merge 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
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
calculateJSD	Calculate the Jensen-Shannon Divergence
calculateJSD-method	Calculate the Jensen-Shannon Divergence
calculateNMDS	Perform non-metric MDS on sample-level data
calculateOverlap	Estimate overlap
calculateOverlap-method	Estimate overlap
calculateRDA	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	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	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
getCCA	Canonical Correspondence Analysis and Redundancy Analysis
getCCA-method	Canonical Correspondence Analysis and Redundancy Analysis
getCrossAssociation	Calculate correlations between features of two experiments.
getCrossAssociation-method	Calculate correlations between features of two experiments.
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 Correspondance analysis
getDPCoA-method	Calculation of Double Principal Correspondance 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
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
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
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	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	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	peerj13075
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	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	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 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
runUnifrac	Calculate weighted or unweighted (Fast) Unifrac distance

-- S --

setTaxonomyRanks	Functions for accessing taxonomic data stored in 'rowData'.
splitByRanks	Agglomerate or merge data using taxonomic information
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	Subset functions
subsetFeatures-method	Subset functions
subsetSamples	Subset functions
subsetSamples-method	Subset functions
subsetTaxa	Subset functions
subsetTaxa-method	Subset functions
summaries	Summarizing microbiome data
summarizeDominance	Summarizing microbiome data
summarizeDominance-method	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	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.
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	dmn_se

-- U --

unsplitByRanks	Agglomerate or merge data using taxonomic information
unsplitByRanks-method	Agglomerate or merge data using taxonomic information
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	These functions will be deprecated. Please use other functions instead.
ZTransform-method	These functions will be deprecated. Please use other functions instead.