callIRevents: Call Intron Retention events from RNA long read alignments

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

Description

This function calls intron retention events from long read data by crossing reference intron intervals and long read alignments. It will:

1. detect reads which overlap at least one intron;

2. compute the proportion of each overlapped intron that is contained in a read;

3. assess whether the read extends beyond left and right intron borders

NB: it takes into account possible gaps and splicing in read alignments.

For more details and usage see vignette('IR-detection-from-Nanopore-data')

Usage

callIRevents(bam, intronGR, flankWidth = 20, keepSecondaryAlignments = FALSE)

Arguments

bam	Either a path to the long read alignments (bam file) from which to call IR events, or a GappedReads object.
intronGR	A GRanges object listing intron genomic intervals to analyse (eg: generated using ['createIntronGR'])
flankWidth	Minimal overlap width read should have over both exon-intron junctions. Should be greater than 0. (Default value: 20 bp - that is 10bp on each side of the junction position)
keepSecondaryAlignments	Whether secondary alignments should be considered (Default: FALSE).

Value

A data.frame listing aligned long read overlapping at least one intron.

Examples

## First, create a GRanges with intron intervals from a reference transcriptome:
## Not run: 
gtf <- "Homo_sapiens.GRCh38.97.gtf"

## End(Not run)
## Then, call intron retention events using alignments in a bam file:
## Not run: 
bamFile <- "myLongReads.bam"
IR_events <- callIRevents(bamFile, intronGR)

## End(Not run)

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