ppSumEIG: RNA Seq Preprocessing Read Summarization

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

RNA Seq Preprocessing Read Summarization

Description

ppSumEIG is a manual wrapper function that provides summarization of read counts for exons, introns and genes using featureCounts. The gtf file passed to this function should first be passed to intronGTFparser to find the location of introns. Reads used for summarization by ppSumEIG should already be mapped, sorted and index using tophat2 and samtools or their wrapper function: ppRawData. The summarized counts produced by ppSumEIG can be further processed using ppFASE, which produces several matrices required by ExonPointer and IntronPointer algorithms for finding alternative splicing events. ppSumEIG need not be run if ppAuto has already been run.

Usage

ppSumEIG(
  folderSRA = FALSE,
  pairedend = FALSE,
  p = 1,
  gtf = gtf,
  srlist = NULL,
  ...
)

Arguments

folderSRA	path of directory containing aligned and indexed bam file folders. (default=current directory)
pairedend	boolean, TRUE if reads are paired-end and FALSE if reads are single-end. (default=FALSE).
p	number of threads to be utilized by Rsubread package. (default=1)
gtf	intron parsed gtf file of the organism.
...	other parameters to be passed to featureCounts.

Value

Lists of gene counts, exon counts and intron counts saved in folderSRA directory as respective Rdata files. (Can be run separately using featureCounts or automatic wrapper function for entire pre-processing: ppAuto)

References

1. Liao Y, Smyth GK, 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.