deprecated: Deprecated functions

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Deprecated functions

Description

Deprecated functions

Usage

plotDegHeatmap(object, ...)

camel(...)

plotCountsPerGene(object, ...)

plotDEGHeatmap(...)

## S4 method for signature 'missing'
plotDegHeatmap(object, results, counts, ...)

plotGeneSaturation(object, ...)

plotGenesDetected(object, ...)

plotMA(...)

plotMeanAverage(...)

plotMeanSD(...)

plotPCA(...)

plotPCACovariates(...)

plotQC(...)

plotRRNAMappingRate(...)

prepareRNASeqTemplate(...)

topTables(...)

writeCounts(..., dir = getOption(x = "acid.export.dir", default = getwd()))

Arguments

...	Additional arguments.
object	Object.
counts	matrix. Count matrix. Normalized counts are recommended.
dir	character(1). Directory path.
`results`	DESeqResults.
`counts`	DESeqTransform.

Value

.Deprecated.

See Also

Deprecated.

Examples

a <- function(...) {
    .Deprecated("b")
    b(...)
}

b <- function(x) {
    x + 1L
}

withCallingHandlers(
    expr = a(1L),
    warning = function(w) {
        print(w)
        invokeRestart("muffleWarning")
    }
)

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.