annotateASevents: AS event annotation

Description Usage Arguments Value References Examples

View source: R/annotateASevents.R

Description

Detect and annotate AS events from GTF. This function borrows code from the IVAS package.

Usage

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annotateASevents(object, gtf.file, num.cores = 1)

Arguments

object

Object of class ASpediaFI

gtf.file

an input GTF file

num.cores

the number of cores for parallel processing

Value

ASpediaFI object with a list of AS event annotations

References

Han, S. et al. (2017). Genome wide discovery of genetic variants affecting alternative splicing patterns in human using bioinformatics method. Genes & Genomics, 39.

Examples

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fi <- new('ASpediaFI')
gtf <- system.file('extdata/GRCh38.subset.gtf', package = 'ASpediaFI')
fi <- annotateASevents(fi, gtf.file = gtf, num.cores = 1)
sapply(events(fi), length)
head(events(fi)$SE)

nachoryu/ASpediaFI documentation built on April 6, 2020, 10:49 a.m.