intronMembershipMatrix: Intron Membership Matrix

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

Intron Membership Matrix

Description

iMM describes association of each intron with meta-features (exons, skipping junctions and flanking junctions) of that gene. It can be generated using a gtf file and a combined junction matrix generated via getJunctionCountMatrix. iMM is a pre-requisite matrix for running iPrnaseq. It should be run only after running readMembershipMatrix.

Usage

intronMembershipMatrix(verbose = TRUE, annotation = annotation)

Arguments

verbose	TRUE
annotation	matrix; contains annotation of exons and introns, created using readMembershipMatrix.

Value

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

• 0 : No association

• 1 : Exon associated with the intron

• 2 : Intron with itself

• 3 : Junction associated with the intron

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.