computeSIRratio: Intron retention levels estimation using short read RNA-seq...

In lbroseus/SIRFindeR: More stable and accurate estimation of Intron Retention levels

Description

This is a wrapper function for computing SIRratio values. It performs all steps required to estimate Intron Retention levels using RNA-seq read alignments and annotation data.

Usage

computeSIRratio(
  gtf,
  keepAnnotatedRI = FALSE,
  chainPath = NULL,
  mappabilityFile = NULL,
  bamFile,
  readLength,
  libraryType,
  junctionFile,
  min_map_cross_junc = 5,
  min_novel_intron_width = 30,
  saveDir,
  verbose = TRUE
)

Arguments

gtf	Reference transcriptome in a gtf/gff file. Used to define introns.
keepAnnotatedRI	Whether intron known as retained in a transcript should be considered (Default: TRUE).
chainPath	(Default: NULL)
mappabilityFile	(eg: wgEncodeCrgMapabilityAlign100mer.bigWig)
bamFile	Path to STAR alignments in a bam file.
readLength	Length of input short reads.
libraryType	Type of the library of RNA-seq data. Either "SE" (single-end) or "PE" (paired-end).
junctionFile	Junction file generated by STAR from the RNA-seq sample.
min_map_cross_junc	Minimal number of supporting reads an intron detected from splice-aware alignments should have (Default: 3).
min_novel_intron_width	Minimal width an intron detected from splice-aware alignments should have (Default: 30).
saveDir	Name for a Project Directory where intermediate and result files will be saved.
verbose	(Default: TRUE)

Value

A data.frame with independent intron intervals and their IRratio2.

lbroseus/SIRFindeR documentation built on Nov. 30, 2020, 11:06 a.m.