Function reference • AcidExperiment

All functions

EnsemblToNcbi() NcbiToEnsembl(): Ensembl-to-NCBI gene identifier mappings

GeneToSymbol(): Gene-to-symbol mappings

TxToGene(): Transcript-to-gene mappings

aggregate() aggregateCols() aggregateRows(): Aggregate

as.SummarizedExperiment(): Coerce to SummarizedExperiment.

autopadZeros(): Autopad zeros

calculateMetrics(): Calculate quality control metrics

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

droplevels2(): Drop unused levels from factors

encode(): Encode using run-length encoding

estimateSizeFactors(): Define size factors from the library sizes, and then apply centering at unity. This ensures that the library size adjustment yields values comparable to those generated after normalization with other sets of size factors.

export(): Export data from R

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 interestingGroups,Annotated-method interestingGroups 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

melt(): Melt data from wide to long format

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(): Strip gene identifier versions

stripTranscriptVersions(): Strip transcript identifier versions

camelCase() dottedCase() snakeCase() upperCamelCase(): Syntactic naming functions

tpm(): Transcripts per million

uniteInterestingGroups(): Unite interesting groups into a single column