scaleOffset: Scale offsets

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

Description

Ensures scale of offsets are consistent with library sizes.

Usage

## S3 method for class 'DGEList'
scaleOffset(y, offset, ...)
## Default S3 method:
scaleOffset(y, offset, ...)

Arguments

y	numeric vector or matrix of counts, or a DGEList object.
offset	numeric vector or matrix of offsets to be scaled. If a vector, its length must equal to the length of y or the number of columns of y. If a matrix, its dimension must equal to the dimension of y.
...	other arguments that are not currently used.

Details

scaleOffset ensures that the scale of offsets are consistent with library sizes. This is done by ensuring that the mean offset for each gene is the same as the mean log-library size. The length or dimensions of offset should be consistent with the number of libraries in y.

Value

scaleOffset.default returns a numeric vector if offset is a vector, a matrix if offset is a matrix or a CompressedMatrix object if offset is a CompressedMatrix. scaleOffset.DGEList computes the scaled offests and store them in the offset component of the input DGEList object.

Author(s)

Aaron Lun, Yunshun Chen

Examples

y <- matrix(rnbinom(40,size=1,mu=100),10,4)
offset <- rnorm(4)
scaleOffset(y, offset)

Example output

Loading required package: limma
[1] 6.724943 7.453119 6.384345 6.939438

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