prepareJunctionSites: Internal function for extracting junction counts from a STAR...

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

Description

This function extracts and merges junctions counts information (for each intron_group) from a STAR junction file. It is intended to be used after calling ['defineIntrons()'], with the same saveDir.

Usage

prepareJunctionSites(
  gtf,
  saveDir,
  junctionFile,
  min_map_cross_junc = 5,
  indIntronsFile = NULL,
  annotIntronsFile = NULL,
  verbose = TRUE
)

Arguments

gtf	Path to a reference transcriptome in a gtf/gff file.
saveDir	Path to a Project directory.
junctionFile	Junction file output by STAR.
min_map_cross_junc	Minimal number of supporting reads an intron detected from splice-aware alignments should have (Default: 3).
indIntronsFile	Path to a file with independent intron intervals as output by ['defineIntrons()'] (Default: NULL). Need not be specified when saveDir is given and contains a file ""independent_introns.txt".
annotIntronsFile	Path to a file with annotated intron intervals as output by ['defineIntrons()'] (Default: NULL). Need not be specified when saveDir is given and contains a file ""all_introns.txt".
verbose	(DEFAULT: TRUE)

Value

Creates and saves files "junction_clusters.txt" and "junction_sites.txt" in saveFolder.

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