DEG: Differentially Expressed Genes

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

Differentially Expressed Genes

Description

A wrapper function of limma package to find differentially expressed genes, given summarized read counts of genes obtained from featureCounts function or preprocessing intructions.

Usage

DEG(geneCount, designM = designM, contrastM = contrastM, Groups = Groups)

Arguments

geneCount	summarized read counts of genes.
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

Saves raw gene counts and log2cpm expression for all genes. Meta-data generated through this function is saved in fit2.Rdata file. Further, annotation of this meta-data is performed by addAnnotationDEG function. Contrast-wise ranking of annotated differentially expressed genes can be obtained using cpmCountsDEG function.

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.