R/AllGenerics.R

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

#' @export
#' @name EnsemblToNcbi
#' @usage EnsemblToNcbi(object, ...)
NULL

#' @export
#' @name GeneToSymbol
#' @usage GeneToSymbol(object, ...)
NULL

#' @export
#' @rdname EnsemblToNcbi
#' @name NcbiToEnsembl
#' @usage NcbiToEnsembl(object, ...)
NULL

#' @export
#' @name TxToGene
#' @usage TxToGene(object, ...)
NULL

#' @export
#' @name aggregate
#' @usage aggregate(x, ...)
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#' @export
#' @rdname aggregate
#' @name aggregateCols
#' @usage aggregateCols(x, ...)
NULL

#' @export
#' @rdname aggregate
#' @name aggregateRows
#' @usage aggregateRows(x, ...)
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#' @export
#' @rdname as.SummarizedExperiment
#' @name as.SummarizedExperiment
#' @usage as.SummarizedExperiment(x, ...)
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#' @export
#' @name autopadZeros
#' @usage autopadZeros(object, ...)
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#' @export
#' @name calculateMetrics
#' @usage calculateMetrics(object, ...)
NULL

#' @export
#' @name combine
#' @usage combine(x, y, ...)
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#' @export
#' @name convertGenesToSymbols
#' @usage convertGenesToSymbols(object, ...)
NULL

#' @export
#' @rdname convertGenesToSymbols
#' @name convertSymbolsToGenes
#' @usage convertSymbolsToGenes(object, ...)
NULL

#' @export
#' @name convertSampleIdsToNames
#' @usage convertSampleIdsToNames(object, ...)
NULL

#' @export
#' @name convertTranscriptsToGenes
#' @usage convertTranscriptsToGenes(object, ...)
NULL

#' @export
#' @name correlation
#' @usage correlation(x, y, ...)
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#' @export
#' @name counts
#' @usage counts(object, ...)
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#' @export
#' @rdname counts
#' @name counts<-
#' @usage counts(object, ...) <- value
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#' @export
#' @name decode
#' @usage decode(x, ...)
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#' @export
#' @name droplevels2
#' @usage droplevels2(x, ...)
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#' @export
#' @name encode
#' @usage encode(x, ...)
NULL

#' @export
#' @name estimateSizeFactors
#' @usage estimateSizeFactors(object, ...)
NULL

#' @export
#' @name export
#' @usage export(object, con, ...)
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#' @export
#' @name geneNames
#' @usage geneNames(object, ...)
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#' @export
#' @name headtail
#' @usage headtail(x, ...)
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#' @export
#' @name humanize
#' @usage humanize(object, ...)
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#' @export
#' @name integerCounts
#' @usage integerCounts(object, ...)
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#' @export
#' @name interestingGroups
#' @usage interestingGroups(object, ...)
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#' @export
#' @rdname interestingGroups
#' @name interestingGroups<-
#' @usage interestingGroups(object, ...)  <- value
NULL

#' @export
#' @name makeSampleData
#' @usage makeSampleData(object, ...)
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#' @export
#' @rdname mapGenes
#' @name mapGenesToRownames
#' @usage mapGenesToRownames(object, ...)
NULL

#' @export
#' @rdname mapGenes
#' @name mapGenesToIds
#' @usage mapGenesToIds(object, ...)
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#' @export
#' @rdname mapGenes
#' @name mapGenesToSymbols
#' @usage mapGenesToSymbols(object, ...)
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#' @export
#' @name matchSampleColumn
#' @usage matchSampleColumn(object, ...)
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#' @export
#' @name melt
#' @usage melt(object, ...)
NULL

#' @export
#' @name metrics
#' @usage metrics(object, ...)
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#' @export
#' @name nonzeroRowsAndCols
#' @usage nonzeroRowsAndCols(object, ...)
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#' @export
#' @name organism
#' @usage organism(object)
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#' @export
#' @rdname organism
#' @name organism<-
#' @usage NULL
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#' @export
#' @name sampleData
#' @usage sampleData(object, ...)
NULL

#' @export
#' @rdname sampleData
#' @name sampleData<-
#' @usage sampleData(object, ...) <- value
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#' @export
#' @name sampleNames
#' @usage sampleNames(object)
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#' @export
#' @rdname sampleNames
#' @name sampleNames<-
#' @usage sampleNames(object) <- value
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#' @export
#' @name selectSamples
#' @usage selectSamples(object, ...)
NULL

#' @export
#' @name sizeFactors
#' @usage sizeFactors(object, ...)
NULL

#' @export
#' @rdname sizeFactors
#' @name sizeFactors<-
#' @usage sizeFactors(object, ...) <- value
NULL

#' @export
#' @name stripGeneVersions
#' @usage stripGeneVersions(object, ...)
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#' @export
#' @name stripTranscriptVersions
#' @usage stripTranscriptVersions(object, ...)
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#' @export
#' @rdname syntactic
#' @name camelCase
#' @usage camelCase(object, ...)
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#' @export
#' @rdname syntactic
#' @name dottedCase
#' @usage dottedCase(object, ...)
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#' @export
#' @rdname syntactic
#' @name snakeCase
#' @usage snakeCase(object, ...)
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#' @export
#' @rdname syntactic
#' @name upperCamelCase
#' @usage upperCamelCase(object, ...)
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#' @export
#' @rdname tpm
#' @name tpm
#' @usage tpm(object, ...)
NULL

#' @export
#' @name uniteInterestingGroups
#' @usage uniteInterestingGroups(object, ...)
NULL