splitIntoGroups {edgeR} | R Documentation |
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.
splitIntoGroups(object) splitIntoGroupsPseudo(pseudo, group, pair)
object |
|
pseudo |
numeric matrix of quantile-adjusted pseudocounts to be split |
group |
factor indicating group to which libraries/samples (i.e. columns of |
pair |
vector of length two stating pair of groups to be split for the pseudocounts |
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.
Davis McCarthy
# 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$counts)<-paste("tagno",1:nrow(d$counts),sep=".") z1<-splitIntoGroups(d) z2<-splitIntoGroupsPseudo(d$counts,d$group,pair=c(1,2))