computeIRrates: Compute observed IR rates from a Long Read experiment

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

Description

This function computes the observed rates of intron retention from a set of long read (genomic) alignments.

Usage

computeIRrates(
  gtf,
  bamFile,
  saveDir,
  flankWidth = 20,
  keepSecondaryAlignments = FALSE
)

Arguments

gtf	Path to a reference transcriptome is a gtf file.
bamFile	Path to a bam file contraining long read alignments.
saveDir	Path to the directory where results sould be saved.
flankWidth	Width of the area on each side of the intron that a read should overlap to be taken into account (Default: 20bp).
keepSecondaryAlignments	Whether secondary alignments should be considered (Default: FALSE).

Value

Saves a data.frame containing observed intron retention rates for each annotated intron in a file named "IRrates.txt" in saveDir.

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