read_bed: Read files containing peaks or genomic regions
In chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Description Usage Arguments Details Value Examples

The following formats are fully supported via their file extensions: .bed, .broadPeak, .narrowPeak, .gff3, .gff2, .gff, and .bedGraph or .bdg. BED3 through BED6 files are supported under the .bed extension. Files without these extensions are supported under the conditions that the first 3 columns correspond to chr, start, and end and that there is either no header column, or it is commented out. Files may be compressed with gzip, and so might end in .narrowPeak.gz, for example. For files with extension support, the rtracklayer::import() function is used to read peaks, so adherence to the mentioned file formats is necessary.

1	read_bed(file_path)

file_path

A path to a file with input peaks/regions. See extended description above for details about file support.

NOTE: Header rows must be commented with # to be ignored. Otherwise, an error may result.

NOTE: A warning is given if any input regions overlap. In the case of enrichment testing with method = 'broadenrich', regions should be disjoint.

Typically, this function will not be used alone, but inside chipenrich().

A GRanges with mcols matching any extra columns.

# Example of generic .txt file with peaks
file = system.file('extdata', 'test_header.txt', package = 'chipenrich')
peaks = read_bed(file)

# Example of BED3
file = system.file('extdata', 'test_assign.bed', package = 'chipenrich')
peaks = read_bed(file)

# Example of narrowPeak
file = system.file('extdata', 'test.narrowPeak', package = 'chipenrich')
peaks = read_bed(file)

# Example of gzipped broadPeak
file = system.file('extdata', 'test.broadPeak.gz', package = 'chipenrich')
peaks = read_bed(file)

# Example of gzipped gff3 Fly peaks
file = system.file('extdata', 'test.gff3.gz', package = 'chipenrich')
peaks = read_bed(file)