Split the Counts or Pseudocounts from a DGEList Object According To Group
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.
## S3 method for class 'DGEList' splitIntoGroups(y, ...) ## Default S3 method: splitIntoGroups(y, group=NULL, ...) splitIntoGroupsPseudo(pseudo, group, pair)
y |
matrix of counts or a |
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. |
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$counts) <- paste("gene", 1:nrow(d$counts), sep=".")
z1 <- splitIntoGroups(d)
z2 <- splitIntoGroupsPseudo(d$counts, d$group, pair=c(1,2))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.