customProDB (version 1.12.0)

Bed2Range: Generate a GRanges objects from BED file.

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

Value

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

Details

Read BED file contain junctions into a GRanges object.

Examples

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