defineIntronicIntervals: Internal function to define sample-specific intronic...

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

Description

This functions determines sample-specific intron borders used for counting intronic reads.

Usage

defineIntronicIntervals(
  gtf,
  saveDir,
  junctionFile,
  keepAnnotatedRI = FALSE,
  min_map_cross_junc = 5,
  min_novel_intron_width = 30,
  verbose = TRUE
)

Arguments

gtf	Path towards a reference transcriptome (gtf or gff format)
saveDir	Path to where output files will be saved
junctionFile	Junction file output by STAR (.tab files)
keepAnnotatedRI	Whether introns annotated as "retained" in the gtf should be considered. (ie: transcripts annotated as "retained_intron" will be removed prior to defining intronic intervals) (Default: TRUE)
min_map_cross_junc	Minimal number of reads supporting a junction to consider a novel intron
min_novel_intron_width	Minimal width for an intronic interval to be kept
verbose	(Default: TRUE)

Value

Outputs curated and independent intronic intervals

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