edgeR (version 3.10.5)

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

splitIntoGroups(object)
splitIntoGroupsPseudo(pseudo, group, pair)

Arguments

object

DGEList, object containing (at least) the elements counts (table of raw counts), group (factor indicating group) and lib.size (numeric vector of library sizes)

pseudo

numeric matrix of quantile-adjusted pseudocounts to be split

group

factor indicating group to which libraries/samples (i.e. columns of pseudo belong; must be same length as ncol(pseudo)

pair

vector of length two stating pair of groups to be split for the pseudocounts

Value

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))