cpmCountsEP: cpmCountsEP

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

cpmCountsEP

Description

This function requires ranking of cassette exon/intron retention events as generated by getPvaluesByContrast to generate raw read counts and log2cpm expression for the ranking of events in a given contrast only.

Usage

cpmCountsEP(filename, designM = designM, Groups, Gcount = Gcount)

Arguments

filename	file in which ExonPointer/IntronPointer ranking of a contrast is saved. *(Filename should be in csv format.)
designM	design matrix.
Groups	list of sample groups. Example: If there are two sample groups with three samples each, 'Groups' should be formed as: c(1, 1, 1, 2, 2, 2).
Gcount	list; contains gene-wise matrix of meta-features read counts times samples, generated by countMatrixGenes.

Value

Read counts and log2cpm expression of ranked cassette exon/intron retention events for the 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.