Bed2Range: Generate a GRanges objects from BED file.

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

Description

Read BED file into a GRanges object. This function requires complete BED file. Go to https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for more information about BED format.

Usage

  Bed2Range(bedfile, skip = 1, covfilter = 5, ...)

Arguments

bedfile	a character contains the path and name of a BED file.
skip	the number of lines of the BED file to skip before beginning to read data, default 1.
covfilter	the number of minimum coverage for the candidate junction, default 5.
...	additional arguments

Details

Read BED file contain junctions into a GRanges object.

Value

a GRanges object containing all candidate junctions from the BED file.

Author(s)

Xiaojing Wang

Examples

bedfile <- system.file("extdata/beds", "junctions1.bed", package="customProDB")
jun <-  Bed2Range(bedfile, skip=1,covfilter=5)
length(jun)

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