cpmCountsDEJ: cpmCountsDEJ

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

cpmCountsDEJ

Description

Save read counts and log2cpm expression of differentially expressed junctions.

Usage

cpmCountsDEJ(
  JunctionMatrix,
  filename,
  designM = designM,
  contrastM = contrastM,
  Groups = Groups
)

Arguments

JunctionMatrix	matrix containing read counts for junctions.
filename	filename in which output of addAnnotationDEJ 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 logcpm expression of given contrast.

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.