readCollection: Given a bunch of region set files, read in all those flat...

In LOLA: Locus overlap analysis for enrichment of genomic ranges

Description

Given a bunch of region set files, read in all those flat (bed) files and create a GRangesList object holding all the region sets. This function is used by readRegionGRL to process annotation objects.

Usage

readCollection(filesToRead, limit = NULL)

Arguments

filesToRead	a vector containing bed files
limit	for testing purposes, limit the number of files read. NULL for no limit (default).

Value

A GRangesList with the GRanges in the filesToRead.

Examples

files = list.files(system.file("extdata", "hg19/ucsc_example/regions",
 package="LOLA"), pattern="*.bed")
regionAnno = readCollection(files)

Example output

Reading 5 files...
1: cpgIslandExt.bed
Skipping (file not found):cpgIslandExt.bed
2: laminB1Lads.bed
Skipping (file not found):laminB1Lads.bed
3: numtSAssembled.bed
Skipping (file not found):numtSAssembled.bed
4: vistaEnhancers.bed
Skipping (file not found):vistaEnhancers.bed
5: vistaEnhancers_colNames.bed
Skipping (file not found):vistaEnhancers_colNames.bed

LOLA documentation built on Nov. 8, 2020, 8:23 p.m.