effectiveLibSizes: Effective Library Sizes

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Extract effective (normalized) library sizes.

Usage

## Default S3 method:
effectiveLibSizes(y, log = FALSE, ...)

Arguments

y	a object of class DGEList, DGEGLM or DGELRT. Alternatively a numeric matrix or an object that can be coerced to a numeric matrix.
log	logical, if TRUE then the library sizes are return on the natural log scale.
...	other arguments are not currently used.

Details

This function extracts normalized library sizes, equal to the original library sizes multiplied by the corresponding normalization factors, from an edgeR data object or fitted model object.

If the object contains a row-specific offsets (i.e., a non-sparse matrix of offsets), then the offsets for the first row are returned.

Value

A numeric matrix of effective (normalized) library sizes. If log=TRUE, then natural log values are returned, equal to library size offsets for a NB log-linear model.

Author(s)

Gordon Smyth

See Also

calcNormFactors

Examples

ngenes <- 100
nsamples <- 4
y <- DGEList(counts=matrix(rnbinom(ngenes*nsamples,size=1,mu=10),ngenes,nsamples))
y <- calcNormFactors(y)
data.frame(y$samples, eff.lib.size=effectiveLibSizes(y))

Example output

Loading required package: limma
        group lib.size norm.factors eff.lib.size
Sample1     1      806    0.9788973     788.9912
Sample2     1     1037    1.0780343    1117.9215
Sample3     1     1073    0.9279603     995.7014
Sample4     1     1012    1.0211767    1033.4309

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.