split.DGEList: Split a DGEList object by a factor of samples (default) or...

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Split a DGEList object by a factor of samples (default) or genes

Description

Split a DGEList object by a factor of samples (default) or genes

Usage

## S3 method for class 'DGEList'
split(x, f, drop = FALSE, bySample = TRUE, sampleDropLevels = TRUE, ...)

splitDGEList(x, f, drop = FALSE, bySample = TRUE, sampleDropLevels = TRUE, ...)

Arguments

x	A DGEList object
f	A factor vector. Other types will be coereced into factors.
drop	Not used now
bySample	Logical, if TRUE, the samples are split. Otherwise, genes are split.
sampleDropLevels	Logical, if TRUE, unused levels in factors in the sample annotation are dropped
...	Not used so far.

Functions

• splitDGEList(): A wrapper of split.DGEList

Examples

y1 <- matrix(rnbinom(1000, mu=5, size=2), ncol=4)
genes1 <- data.frame(GeneSymbol=sprintf("Gene%d", 1:nrow(y1)),
  GeneType=gl(5,50))
rownames(y1) <- rownames(genes1) <- 1:nrow(y1)
anno1 <- data.frame(treatment=gl(2,2, labels=c("ctrl", "tmt")),
    donor=factor(rep(c(1,2), each=2)))
d1 <- DGEList(counts=y1, genes=genes1, samples=anno1)

d1SampleSplit <- split(d1, d1$samples$donor)
d1GeneSplit <- split(d1, d1$genes$GeneType, bySample=FALSE)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.