SharedJunc: Generate shared junctions dataset from multiple BED files

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Description

Load multiple BED files and output a GRange object with junctions present in multiple samples.

Usage

  SharedJunc(juns, share_num = 2, ...)

Arguments

juns	a list of GRanges object which input from multiple VCF files using function InputVcf.
share_num	Junctions must occurs in this number of samples to be consider. Two options, percentage format or sample number.
...	additional arguments

Details

This function allows to limit junctions that are present in at least m out of n BED files.

Value

a GRange object that contains the shared junctions

Author(s)

Xiaojing Wang

Examples

path <- system.file("extdata/beds", package="customProDB")
bedFiles<- paste(path, '/', list.files(path, pattern="*bed$"), sep='')
juncs <- lapply(bedFiles, function(x) Bed2Range(x, skip=1, covfilter=5))
shared <- SharedJunc(juncs, share_num=2)
shared

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.