Microbiome analysis


[Up] [Top]

Documentation for package ‘mia’ version 1.12.0

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