cpmCountsDEG: cpmCountsDEG

In harshsharma-cb/FASE: Analysis of RNA-Sequencing data using FASE (Finding Alternative Splicing Events).

cpmCountsDEG

Description

Generates read counts and log2cpm expression for differentially expressed genes for a given contrast, using output of addAnnotationDEG function.

Usage

cpmCountsDEG(
  geneCount,
  filename,
  designM = designM,
  contrastM = contrastM,
  Groups = Groups
)

Arguments

geneCount	summarized read counts of genes.
filename	filename in which output of addAnnotationDEG is saved.
designM	design matrix required by limma
contrastM	contrast matrix required by limma.
Groups	list of sample groups. Example: If there are two sample groups with three samples each, 'Groups' should be formed as: numeric: c(1, 1, 1, 2, 2, 2)

Value

Read counts and log2cpm expression of given contrast for ranked differentially expressed genes.

References

1. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2009)

harshsharma-cb/FASE documentation built on Aug. 6, 2023, 1:37 a.m.