R: Counts per Million or Reads per Kilobase per Million

cpm {edgeR}

R Documentation

Counts per Million or Reads per Kilobase per Million

Description

Computes counts per million (CPM) or reads per kilobase per million (RPKM) values.

Usage

## S3 method for class 'DGEList'
cpm(x, normalized.lib.sizes=TRUE, log=FALSE, prior.count=0.25, ...)
## Default S3 method:
cpm(x, lib.size=NULL, log=FALSE, prior.count=0.25, ...)
rpkm(x, gene.length, normalized.lib.sizes=TRUE, log=FALSE, prior.count=0.25)

Arguments

`x`	matrix of counts or a `DGEList` object
`normalized.lib.sizes`	logical, use normalized library sizes?
`lib.size`	library size, defaults to `colSums(x)`.
`log`	logical, if `TRUE` then `log2` values are returned.
`prior.count`	average count to be added to each observation to avoid taking log of zero. Used only if `log=TRUE`.
`gene.length`	vector of length `nrow(x)` giving gene length in bases.
`...`	other arguments are not currently used

Details

CPM or RPKM values are useful descriptive measures for the expression level of a gene or transcript. By default, the normalized library sizes are used in the computation for DGEList objects but simple column sums for matrices.

If log-values are computed, then a small count, given by prior.count but scaled to be proportional to the library size, is added to x to avoid taking the log of zero.

Value

numeric matrix of CPM or RPKM values.

Note

aveLogCPM(x), rowMeans(cpm(x,log=TRUE)) and log2(rowMeans(cpm(x)) all give slightly different results.

Author(s)

Davis McCarthy, Gordon Smyth

Examples

y <- matrix(rnbinom(20,size=1,mu=10),5,4)
cpm(y)
d <- DGEList(counts=y, lib.size=1001:1004)
cpm(d)
cpm(d,log=TRUE)

[Package edgeR version 3.4.2 Index]