read_bed {plyranges} | R Documentation |
This is a lightweight wrapper to the import family of functions defined in rtracklayer.
Read common interval based formats as GRanges.
read_bed(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL) read_bed_graph( file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL ) read_narrowpeaks( file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL )
file |
A path to a file or a connection. |
col_names |
An optional character vector for including additional
columns in |
genome_info |
An optional character string or a Ranges object that contains information about the genome build. For example the USSC identifier "hg19" will add build information to the returned GRanges. |
overlap_ranges |
An optional Ranges object. Only the intervals in the file that overlap the Ranges will be returned. |
This is a lightweight wrapper to the import family
of functions defined in rtracklayer.
The read_narrowpeaks
function parses the ENCODE narrowPeak BED format (see
https://genome.ucsc.edu/FAQ/FAQformat.html#format12 for details.). As
such the parser expects four additional columns called (corresponding to
the narrowPeaks spec):
signalValue
pValue
qValue
peak
A GRanges object
rtracklayer::BEDFile()
test_path <- system.file("tests", package = "rtracklayer") bed_file <- file.path(test_path, "test.bed") gr <- read_bed(bed_file) gr gr <- read_bed(bed_file, genome_info = "hg19") gr olap <- as_granges(data.frame(seqnames = "chr7", start = 1, end = 127473000)) gr <- read_bed(bed_file, overlap_ranges = olap) # bedGraph bg_file <- file.path(test_path, "test.bedGraph") gr <- read_bed_graph(bg_file) gr # narrowpeaks np_file <- system.file("extdata", "demo.narrowPeak.gz", package="rtracklayer") gr <- read_narrowpeaks(np_file, genome_info = "hg19") gr