meltCounts: Melt Count Matrix to Long Format

Description Usage Arguments Value See Also Examples

Description

Melt Count Matrix to Long Format

Usage

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## S4 method for signature 'SummarizedExperiment'
meltCounts(object, assay = 1L,
  nonzeroGenes = FALSE, trans = c("identity", "log2", "log10"))

Arguments

object

Object.

assay

scalar. Name or index of count matrix slotted in SummarizedExperiment::assays(). When passing in a string, the name must be defined in SummarizedExperiment::assayNames().

nonzeroGenes

boolean. Return only non-zero genes.

trans

string. Apply a log transformation (e.g. log2(x + 1L)) to the count matrix prior to melting, if desired. Use "identity" to return unmodified (default).

Value

grouped_df, grouped by colname (e.g. sample ID) and rowname (e.g. gene ID).

See Also

reshape2::melt().

Examples

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data(rse, package = "basejump.data")
x <- meltCounts(rse)
print(x)

steinbaugh/basejump.experiment documentation built on Nov. 5, 2018, 10:36 p.m.