splitIntoGroups: Split the Counts or Pseudocounts from a DGEList Object...

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Split the counts from a DGEList object according to group, creating a list where each element consists of a numeric matrix of counts for a particular experimental group. Given a pair of groups, split pseudocounts for these groups, creating a list where each element is a matrix of pseudocounts for a particular gourp.

Usage

## S3 method for class 'DGEList'
splitIntoGroups(y, ...)
## Default S3 method:
splitIntoGroups(y, group=NULL, ...)
splitIntoGroupsPseudo(pseudo, group, pair)

Arguments

y	matrix of counts or a DGEList object.
group	vector or factor giving the experimental group/condition for each library.
pseudo	numeric matrix of quantile-adjusted pseudocounts to be split
pair	vector of length two stating pair of groups to be split for the pseudocounts
...	other arguments that are not currently used.

Value

splitIntoGroups outputs a list in which each element is a matrix of count counts for an individual group. splitIntoGroupsPseudo outputs a list with two elements, in which each element is a numeric matrix of (pseudo-)count data for one of the groups specified.

Author(s)

Davis McCarthy

Examples

# generate raw counts from NB, create list object
y <- matrix(rnbinom(80, size=1, mu=10), nrow=20)
d <- DGEList(counts=y, group=rep(1:2, each=2), lib.size=rep(c(1000:1001), 2))
rownames(d$counts) <- paste("gene", 1:nrow(d$counts), sep=".")
z1 <- splitIntoGroups(d)
z2 <- splitIntoGroupsPseudo(d$counts, d$group, pair=c(1,2))

Example output

Loading required package: limma

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.