cpm {edgeR} | R Documentation

## Counts per Million or Reads per Kilobase per Million

### Description

Compute counts per million (CPM) or reads per kilobase per million (RPKM).

### Usage

    ## S3 method for class 'DGEList'
    cpm(y, normalized.lib.sizes = TRUE,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'SummarizedExperiment'
    cpm(y, normalized.lib.sizes = TRUE,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'DGEGLM'
    cpm(y, log = FALSE, shrunk = TRUE, ...)
    ## Default S3 method:
    cpm(y, lib.size = NULL, offset=NULL,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'DGEList'
    rpkm(y, gene.length = NULL, normalized.lib.sizes = TRUE,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'SummarizedExperiment'
    rpkm(y, gene.length = NULL, normalized.lib.sizes = TRUE,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'DGEGLM'
    rpkm(y, gene.length, log = FALSE, shrunk = TRUE, ...)
    ## Default S3 method:
    rpkm(y, gene.length, lib.size = NULL, offset=NULL,
           log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'DGEList'
    cpmByGroup(y, group = NULL, dispersion = NULL, ...)
    ## S3 method for class 'SummarizedExperiment'
    cpmByGroup(y, group = NULL, dispersion = NULL, ...)
    ## Default S3 method:
    cpmByGroup(y, group = NULL, dispersion = 0.05,
           offset = NULL, weights = NULL, log = FALSE, prior.count = 2, ...)
    ## S3 method for class 'DGEList'
    rpkmByGroup(y, group = NULL, gene.length = NULL, dispersion = NULL, ...)
    ## S3 method for class 'SummarizedExperiment'
    rpkmByGroup(y, group = NULL, gene.length = NULL, dispersion = NULL, ...)
    ## Default S3 method:
    rpkmByGroup(y, group = NULL, gene.length, dispersion = 0.05,
           offset = NULL, weights = NULL, log = FALSE, prior.count = 2, ...)

### Arguments

`y` | a matrix-like object containing counts. Can be a numeric matrix, a `DGEList` object, a `SummarizedExperiment` object with a `"counts"` assay, or any object that can be coerced to a matrix by `as.matrix`. For `cpm` and `rpkm`, it can also be a `DGEGLM` or `DGELRT` object.
`normalized.lib.sizes` | logical, use normalized library sizes?
`lib.size` | library size, defaults to `colSums(y)`. Ignored if `offset` is specified.
`offset` | numeric matrix of same size as `y`, or a vector of length `ncol(y)`, representing library sizes on the log scale. Can also be a scalar for `cpmByGroup.default` and `rpkmByGroup.default`. If specified, then takes precedence over `lib.size`.
`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`.
`shrunk` | logical, if `TRUE` then the usual coefficients from the fitted object will be used, if `FALSE` then the unshrunk coefficients will be used.
`gene.length` | vector of length `nrow(y)` giving gene length in bases, or the name of the column `y$genes` containing the gene lengths.
`group` | factor giving group membership for columns of `y`. Defaults to `y$sample$group` for the `DGEList` method and to a single level factor for the default method.
`dispersion` | numeric vector of negative binomial dispersions.
`weights` | numeric vector or matrix of non-negative quantitative weights. Can be a vector of length equal to the number of libraries, or a matrix of the same size as `y`.
`...` | other arguments are not used.

### Details

CPM or RPKM values are useful descriptive measures for the expression level of a gene. 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 `y` to avoid taking the log of zero.

The `rpkm` methods for `DGEList`, `DGEGLM` or `DGELRT` objects will try to find the gene lengths in a column of `y$genes` called `Length` or `length`. Failing that, it will look for any column name containing `"length"` in any capitalization.

The `cpm` and `rpkm` methods for `DGEGLM` and `DGELRT` fitted model objects return fitted CPM or RPKM values. If `shrunk=TRUE`, then the CPM or RPKM values will reflect the `prior.count` input to the original linear model fit. If `shrunk=FALSE`, then the CPM or RPKM values will be computed with `prior.count=0`. Note that the latter could result in taking the log of near-zero values if `log=TRUE`.

`cpmByGroup` and `rpkmByGroup` compute group average values on the unlogged scale.

### Value

A numeric matrix of CPM or RPKM values, on the log2 scale if `log=TRUE`. `cpm` and `rpkm` produce matrices of the same size as `y`. If `y` was a data object, then observed values are returned. If `y` was a fitted model object, then fitted values are returned.

`cpmByGroup` and `rpkmByGroup` produce matrices with a column for each level of `group`.

### Note

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

### Author(s)

Davis McCarthy, Gordon Smyth, Yunshun Chen, Aaron Lun

### See Also

`aveLogCPM`

### 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)

    d$genes <- data.frame(Length=c(1000,2000,500,1500,3000))
    rpkm(d)

    cpmByGroup(d, group=c(1,1,2,2))

    rpkmByGroup(d, group=c(1,1,2,2))

[Package edgeR version 3.32.1 Index]