readMembershipMatrix: Read Membership Matrix

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

Read Membership Matrix

Description

RMM describes association of each exon with meta-features (introns, skipping junctions and flanking junctions) of that gene. It can be generated using a gtf file and a combined junction matrix generated via getJunctionCountMatrix. RMM is a pre-requisite matrix for running EPrnaseq.

Usage

readMembershipMatrix(gtf, JunctionMatrix = JunctionMatrix)

Arguments

gtf	gtf file of the organism.
JunctionMatrix	junction matrix contains read counts of each junction mapped by tophat2 alongwith their annotation.

Value

readMembershipMatrix creates a gene-wise list which is saved by default as RMM.Rdata. Each gene is represented by a matrix of meta-features times the number of exons in gene.
A number is assigned for each meta-feature association to exons in the gene as:

• 0 : No association

• 0.5: Skipping junction to the exon

• 1 : Exon with itself

• 2 : Flanking junction to the exon

• 3 : Intron associated with the exon

References

1. F. Hoffgaard, P. Weil, K. Hamacher. BioPhysConnectoR: Connecting Sequence Information and Biophysical Models. BMC Bioinformatics volume 11, Article number: 199 (2010).

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