countMatrixGenes: Count Matrix Genes

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

Count Matrix Genes

Description

This function creates association of metafeatures such as exons, introns and junctions times sample for each gene. It requires a junction matrix, annotation matrix (generated by default using readMembershipMatrix) and summarized exon and intron read counts. It should be run only after running readMembershipMatrix and intronMembershipMatrix.

Usage

countMatrixGenes(
  JunctionMatrix,
  annotation,
  intronList = c(intron_A, intron_B, intron_C),
  exonList = c(out_A, out_B, out_C)
)

Arguments

JunctionMatrix	matrix of junction read counts times samples, generated by getJunctionCountMatrix.
annotation	gene features and meta-featues annotation file generated by readMembershipMatrix, saved by default as Annotation.Rdata.
intronList	intron read counts per gene generated by Rsubread package and saved in counts_introns.Rdata file, as per preprocessing instructions.
exonList	exon read counts per gene generated by Rsubread package and saved in counts_exons.Rdata file, as per preprocessing instructions.

Value

Gcount list contains gene-wise read count summarization of meta-features times samples in the study. The output is saved as Gcount.Rdata.

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