SharedJunc: Generate shared junctions dataset from multiple BED files

In chambm/customProDB: Generate customized protein databases from NGS 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, ext_up = 100, ext_down = 100, ...)

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.
ext_up	upstream extension from the junction point, Default is 100nt.
ext_down	downstream extension from the junction point, Default is 100nt.
...	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, ext_up=100, ext_down=100)
shared

chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.