Man pages for acidgenomics/r-acidexperiment
Acid Genomics Summarized Experiment

AcidExperiment-packageAcidExperiment
AcidExperimentTestsURLAcidExperiment test data URL
aggregateAggregate
aggregateColsAggregate columns
aggregateRowsAggregate rows
autopadZerosAutopad zeros
calculateMetricsCalculate quality control metrics
coerceCoercion methods
combineCombine multiple objects
convertGenesToSymbolsConvert genes to symbols
convertSampleIDsToNamesConvert sample identifiers to names
convertTranscriptsToGenesConvert transcripts to genes
correlationCorrelation
countsCounts
decodeDecode column data that uses run-length encoding
detectLanesDetect sequencing lanes
droplevelsDrop unused levels from factors
encodeEncode using run-length encoding
Ensembl2EntrezEnsembl-to-Entrez gene identifier mappings
estimateSizeFactorsEstimate size factors
exportExport
Gene2SymbolGene-to-symbol mappings
geneNamesGene names
headtailReturn the first and last parts of an object
humanizeHumanize an R object
importSampleDataImport sample metadata
integerCountsInteger counts
interestingGroupsInteresting groups
makeSampleDataMake sample data
makeSummarizedExperimentMake a SummarizedExperiment object
mapGenesMap genes
matchesGene2SymbolCheck that user-defined gene input matches expected values
matchesInterestingGroupsCheck that interesting groups match a defined value
matchInterestingGroupsMatch interesting groups
matchSampleColumnMatch sample identifier column
meltMelt columns into key-value pairs
metricsQuality control metrics
microplateMicrotiter plate well identifiers
minimalSampleDataMinimal sample data
nonzeroRowsAndColsSubset object to keep only non-zero rows and columns
organismOrganism
reexportsObjects exported from other packages
sampleDataSample data
sampleNamesSample names
sanitizeSampleDataSanitize sample data
selectSamplesSelect samples
sizeFactorsSize factors
stripVersionsStrip transcript identifier versions
syntacticSyntactic naming functions
tpmTranscripts per million
Tx2GeneTranscript-to-gene identifier mappings
uniteInterestingGroupsUnite interesting groups into a single column
acidgenomics/r-acidexperiment documentation built on June 12, 2021, 7:58 p.m.