spliceEvent {ribosomeProfilingQC} | R Documentation |
Get differentical usage of alternative Translation Initiation Sites, alternative Polyadenylation Sites or alternative splicing sites
spliceEvent(coverage, group1, group2)
coverage |
Coverages of feature region with extensions. Output of coverageDepth |
group1, group2 |
The sample names of group 1 and group 2 |
A GRanges object of splice events.
## 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)