These functions will be deprecated. Please use other functions instead.

These functions will be deprecated. Please use other functions instead.

cluster(x, ...)

# S4 method for class 'SummarizedExperiment'
cluster(x, ...)

addTaxonomyTree(x, ...)

# S4 method for class 'SummarizedExperiment'
addTaxonomyTree(x, ...)

taxonomyTree(x, ...)

# S4 method for class 'SummarizedExperiment'
taxonomyTree(x, ...)

mergeRows(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeRows(x, ...)

# S4 method for class 'TreeSummarizedExperiment'
mergeRows(x, ...)

mergeCols(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeCols(x, ...)

# S4 method for class 'TreeSummarizedExperiment'
mergeCols(x, ...)

mergeFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeFeatures(x, ...)

# S4 method for class 'TreeSummarizedExperiment'
mergeFeatures(x, ...)

mergeSamples(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeSamples(x, ...)

# S4 method for class 'TreeSummarizedExperiment'
mergeSamples(x, ...)

mergeFeaturesByRank(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeFeaturesByRank(x, ...)

# S4 method for class 'SingleCellExperiment'
mergeFeaturesByRank(x, ...)

mergeFeaturesByPrevalence(x, ...)

# S4 method for class 'SummarizedExperiment'
mergeFeaturesByPrevalence(x, ...)

getExperimentCrossAssociation(x, ...)

# S4 method for class 'MultiAssayExperiment'
getExperimentCrossAssociation(x, ...)

# S4 method for class 'SummarizedExperiment'
getExperimentCrossAssociation(x, ...)

# S4 method for class 'TreeSummarizedExperiment'
mergeFeaturesByRank(x, ...)

testExperimentCrossAssociation(x, ...)

# S4 method for class 'ANY'
testExperimentCrossAssociation(x, ...)

testExperimentCrossCorrelation(x, ...)

# S4 method for class 'ANY'
testExperimentCrossCorrelation(x, ...)

getExperimentCrossCorrelation(x, ...)

# S4 method for class 'ANY'
getExperimentCrossCorrelation(x, ...)

loadFromBiom(...)

loadFromQIIME2(...)

readQZA(...)

loadFromMothur(...)

loadFromMetaphlan(...)

loadFromHumann(...)

countDominantFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
countDominantFeatures(x, ...)

subsetByRareTaxa(x, ...)

# S4 method for class 'ANY'
subsetByRareTaxa(x, ...)

subsetByRareFeatures(x, ...)

# S4 method for class 'ANY'
subsetByRareFeatures(x, ...)

subsetByPrevalentTaxa(x, ...)

# S4 method for class 'ANY'
subsetByPrevalentTaxa(x, ...)

subsetByPrevalentFeatures(x, ...)

# S4 method for class 'ANY'
subsetByPrevalentFeatures(x, ...)

countDominantTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
countDominantTaxa(x, ...)

full_join(x, ...)

# S4 method for class 'ANY'
full_join(x, ...)

inner_join(x, ...)

# S4 method for class 'ANY'
inner_join(x, ...)

left_join(x, ...)

# S4 method for class 'ANY'
left_join(x, ...)

right_join(x, ...)

# S4 method for class 'ANY'
right_join(x, ...)

plotNMDS(x, ...)

estimateDivergence(x, ...)

# S4 method for class 'SummarizedExperiment'
estimateDivergence(x, ...)

meltAssay(x, ...)

# S4 method for class 'SummarizedExperiment'
meltAssay(x, ...)

transformSamples(x, ...)

# S4 method for class 'SummarizedExperiment'
transformSamples(x, ...)

ZTransform(x, ...)

# S4 method for class 'SummarizedExperiment'
ZTransform(x, ...)

relAbundanceCounts(x, ...)

# S4 method for class 'SummarizedExperiment'
relAbundanceCounts(x, ...)

transformCounts(x, ...)

transformFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
transformFeatures(x, ...)

getUniqueFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
getUniqueFeatures(x, ...)

getUniqueTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
getUniqueTaxa(x, ...)

getTopFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
getTopFeatures(x, ...)

getTopTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
getTopTaxa(x, ...)

getRareFeatures(x, ...)

# S4 method for class 'ANY'
getRareFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
getRareFeatures(x, ...)

getRareTaxa(x, ...)

# S4 method for class 'ANY'
getRareTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
getRareTaxa(x, ...)

getPrevalentFeatures(x, ...)

# S4 method for class 'ANY'
getPrevalentFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
getPrevalentFeatures(x, ...)

getPrevalentTaxa(x, ...)

# S4 method for class 'ANY'
getPrevalentTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
getPrevalentTaxa(x, ...)

subsampleCounts(x, ...)

# S4 method for class 'SummarizedExperiment'
subsampleCounts(x, ...)

addPerSampleDominantFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
addPerSampleDominantFeatures(x, ...)

addPerSampleDominantTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
addPerSampleDominantTaxa(x, ...)

perSampleDominantFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
perSampleDominantFeatures(x, ...)

perSampleDominantTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
perSampleDominantTaxa(x, ...)

makePhyloseqFromTreeSE(x, ...)

# S4 method for class 'SummarizedExperiment'
makePhyloseqFromTreeSE(x)

# S4 method for class 'TreeSummarizedExperiment'
makePhyloseqFromTreeSE(x)

makePhyloseqFromTreeSummarizedExperiment(x)

# S4 method for class 'ANY'
makePhyloseqFromTreeSummarizedExperiment(x)

makeTreeSummarizedExperimentFromPhyloseq(x)

# S4 method for class 'ANY'
makeTreeSummarizedExperimentFromPhyloseq(x)

makeTreeSEFromBiom(...)

makeTreeSummarizedExperimentFromBiom(...)

makeTreeSEFromDADA2(...)

makeTreeSummarizedExperimentFromDADA2(...)

makeTreeSEFromPhyloseq(x)

estimateEvenness(x, ...)

# S4 method for class 'ANY'
estimateEvenness(x, ...)

estimateRichness(x, ...)

# S4 method for class 'ANY'
estimateRichness(x, ...)

estimateDiversity(x, ...)

# S4 method for class 'ANY'
estimateDiversity(x, ...)

estimateFaith(x, ...)

# S4 method for class 'ANY'
estimateFaith(x, ...)

estimateDominance(x, ...)

# S4 method for class 'ANY'
estimateDominance(x, ...)

subsetSamples(x, ...)

subsetFeatures(x, ...)

subsetTaxa(x, ...)

# S4 method for class 'SummarizedExperiment'
subsetSamples(x, ...)

# S4 method for class 'SummarizedExperiment'
subsetFeatures(x, ...)

# S4 method for class 'SummarizedExperiment'
subsetTaxa(x, ...)

relabundance(x, ...)

relabundance(x) <- value

# S4 method for class 'SummarizedExperiment'
relabundance(x)

# S4 method for class 'SummarizedExperiment'
relabundance(x) <- value

runOverlap(x, ...)

# S4 method for class 'SummarizedExperiment'
runOverlap(x, ...)

calculateOverlap(x, ...)

# S4 method for class 'ANY'
calculateOverlap(x, ...)

calculateJSD(x, ...)

# S4 method for class 'ANY'
calculateJSD(x, ...)

runJSD(x, ...)

# S4 method for class 'SummarizedExperiment'
runJSD(x, ...)

calculateUnifrac(x, ...)

# S4 method for class 'ANY'
calculateUnifrac(x, ...)

runUnifrac(mat, tree, ...)

Arguments

x

A SummarizedExperiment object.

...

Additional parameters. See dedicated function.

value

a matrix to store as the ‘relabundance’ assay

mat

An abundance matrix

tree

A phylogenetic tree