All functions

Ensembl2Entrez() Entrez2Ensembl()

Ensembl-to-Entrez gene identifier mappings

Gene2Symbol()

Gene-to-symbol mappings

Tx2Gene()

Transcript-to-gene identifier mappings

aggregate()

Aggregate

aggregateCols()

Aggregate columns

aggregateRows()

Aggregate rows

autopadZeros()

Autopad zeros

calculateMetrics()

Calculate quality control metrics

as.SummarizedExperiment()

Coercion methods

combine()

Combine multiple objects

convertGenesToSymbols() convertSymbolsToGenes()

Convert genes to symbols

convertSampleIDsToNames()

Convert sample identifiers to names

convertTranscriptsToGenes()

Convert transcripts to genes

correlation()

Correlation

counts() `counts<-`()

Counts

decode()

Decode column data that uses run-length encoding

detectLanes()

Detect sequencing lanes

droplevels()

Drop unused levels from factors

encode()

Encode using run-length encoding

estimateSizeFactors()

Estimate size factors

export()

Export

geneNames()

Gene names

headtail()

Return the first and last parts of an object

humanize()

Humanize an R object

importSampleData()

Import sample metadata

integerCounts()

Integer counts

interestingGroups() `interestingGroups<-`()

Interesting groups

makeSampleData()

Make sample data

makeSummarizedExperiment()

Make a SummarizedExperiment object

mapGenesToRownames() mapGenesToIDs() mapGenesToSymbols()

Map genes

matchInterestingGroups()

Match interesting groups

matchSampleColumn()

Match sample identifier column

matchesGene2Symbol()

Check that user-defined gene input matches expected values

matchesInterestingGroups()

Check that interesting groups match a defined value

melt()

Melt columns into key-value pairs

metrics()

Quality control metrics

microplate()

Microtiter plate well identifiers

minimalSampleData()

Minimal sample data

nonzeroRowsAndCols()

Subset object to keep only non-zero rows and columns

organism()

Organism

sampleData() `sampleData<-`() sampleNames(<SummarizedExperiment>)

Sample data

sampleNames() `sampleNames<-`()

Sample names

sanitizeSampleData()

Sanitize sample data

selectSamples()

Select samples

sizeFactors() `sizeFactors<-`()

Size factors

stripGeneVersions() stripTranscriptVersions()

Strip transcript identifier versions

camelCase() dottedCase() snakeCase() upperCamelCase()

Syntactic naming functions

tpm()

Transcripts per million

uniteInterestingGroups()

Unite interesting groups into a single column