spliceEvent: Get splicing events

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Get splicing events

Description

Get differentical usage of alternative Translation Initiation Sites, alternative Polyadenylation Sites or alternative splicing sites

Usage

spliceEvent(coverage, group1, group2)

Arguments

coverage	Coverages of feature region with extensions. Output of coverageDepth
group1, group2	The sample names of group 1 and group 2

Value

A GRanges object of splice events.

Examples

## Not run: 
path <- system.file("extdata", package="ribosomeProfilingQC")
RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
coverage <- coverageDepth(RPFs, gtf=gtf,
                  level="gene", region="feature with extension")
group1 <- c("RPF.KD1.1", "RPF.KD1.2")
group2 <- c("RPF.WT.1", "RPF.WT.2")
se <- spliceEvent(coverage, group1, group2)

## End(Not run)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.