computeSizeFactors: computeSizeFactors
In gstricker/GenoGAM: A GAM based framework for analysis of ChIP-Seq data

Description Usage Arguments Value Author(s) Examples

The function computes the size factors for given factor groups based on the DESeq2 package.

1	computeSizeFactors(ggd, factorGroups = NULL)

`ggd`	A GenoGAMDataSet object.
`factorGroups`	A list of grouped IDs (same as the colnames of the GenoGAMDataSet object). Each element of the list represents a group of samples within which size factors are computed. If NULL all samples are regarded to belong to one group.

A GenoGAMDataSet object, where the sizeFactors slot is updated.

Georg Stricker georg.stricker@in.tum.de

ggd <- makeTestGenoGAMDataSet()
ggd <- computeSizeFactors(ggd)
sizeFactors(ggd)
groups <- list(c("wt_1", "wt_2"), c("mutant_1", "mutant_2"))
ggd <- computeSizeFactors(ggd, factorGroups = groups)
sizeFactors(ggd)