computeSizeFactors

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.
Size factors are not computed between groups.

factorGroups


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


This package allows statistical analysis of genome-wide
data with smooth functions using generalized additive models
based on the implementation from the R-package 'mgcv'. It
provides methods for the statistical analysis of ChIP-Seq data
including inference of protein occupancy, and pointwise and
region-wise differential analysis. Estimation of dispersion and
smoothing parameters is performed by cross-validation. Scaling
of generalized additive model fitting to whole chromosomes is
achieved by parallelization over overlapping genomic intervals.

Georg Stricker

GenoGAM

A GAM based framework for analysis of ChIP-Seq data

computeSizeFactors function

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

computeSizeFactors: computeSizeFactors

Description

Usage

Arguments

Value

Examples