edge (version 2.4.2)

splitIntoGroups: Split the Counts or Pseudocounts from a DGEList Object According To Group

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, ...)
## S3 method for class 'default':
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.

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))