DEJ: Differentially Expressed Junctions

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

Differentially Expressed Junctions

Description

Find differentially expressed junctions, provided a junction matrix as input (generated by getJunctionCountMatrix). This function uses standard limma package (eBayes) to find differentially expressed junctions.

Usage

DEJ(JunctionMatrix, designM = designM, contrastM = contrastM, Groups = Groups)

Arguments

JunctionMatrix	matrix containing read counts for junctions, obtained using getJunctionCountMatrix .
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

The output is ranked differentially expressed junctions. Meta-data is saved as fit2.Rdata in folderSRA directory. The ranking can be annotated using addAnnotationDEJ. The annotated and ranked differentially expressed junctions for a given contrast (as given in contrast matrix) can be saved using cpmCountsDEJ

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.