ppFASE: Alternative Splicing Pre-processing

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

Alternative Splicing Pre-processing

Description

Alternative Splicing preprocessing function. This function creates several prerequisite matrices for related to meta-features:junction matrix (by combining output of tophat2: junction.bed), ReadMembershipMatrix (RMM), IntronMembershipMatrix (IMM) and Gcount matrix in order to run ExonPointer and IntronPointer algorithms. ppFASE should be run only after tophat2 (or its wrapper function: ppRawData) has mapped all the raw read files and the reads have been summarized using featureCounts (or its wrapper function: ppSumEIG).

Usage

ppFASE(
  folderSRA = FALSE,
  gtf = gtf,
  exonCount = exonCount,
  intronCount = intronCount,
  JunctionMatrix = JunctionMatrix
)

Arguments

folderSRA	directory containing fastq or SRA files.
gtf	intron parsed gtf file of the organism.
JunctionMatrix	junction count matrix. If ppRawData has been run, JunctionMatrix is saved in JunctionCounts.Rdata.
exonCounts	list of summarized exon counts. If ppSumEIG has been run, exonCounts are saved in counts_exons.Rdata.
intronCounts	list of summarized intron counts. If ppSumEIG has been run, intronCounts are saved in counts_introns.Rdata.

Value

1. Junction Matrix: Matrix with Junction count reads and their annotation. (Can be run separately using getJunctionCountMatrix)

2. RMM : ReadMembershipMatrix. (Can be run separately using readMembershipMatrix or wrapper function: ppAuto)

3. iMM : intronMembershipMatrix. (Can be run separately using intronMembershipMatrix or wrapper function: ppAuto)

4. Gcount : A list of gene-wise read count summarization of meta-features times samples in the study. (Can be run separately using countMatrixGenes or wrapper function: ppAuto)

References

Liao Y., Smyth G.K., Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research, 47, e47 (2019).

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