splitIntoGroups {edgeR} | R Documentation

## 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, ...)
    ## 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))

[Package edgeR version 3.28.1 Index]