valr (version 0.5.0)

read_bed: Read BED and related files.

Description

read functions for BED and related formats. Filenames can be local file or URLs. The read functions load data into tbls with consistent chrom, start and end colnames.

Usage

read_bed(filename, n_fields = 3, col_types = bed12_coltypes,
  sort = TRUE, ...)
read_bed12(filename, ...)
read_bedgraph(filename, ...)
read_narrowpeak(filename, ...)
read_broadpeak(filename, ...)

Arguments

filename

file or URL

n_fields

number fields in the BED file

col_types

column type spec for readr::read_tsv()

sort

sort the tbl by chrom and start

...

options to pass to readr::read_tsv()

Value

tbl_interval()

Details

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

https://genome.ucsc.edu/goldenPath/help/bedgraph.html

https://genome.ucsc.edu/FAQ/FAQformat.html#format12

https://genome.ucsc.edu/FAQ/FAQformat.html#format13

See Also

Other read functions: read_genome, read_vcf

Examples

# NOT RUN {
# read_bed assumes 3 field BED format.
read_bed(valr_example('3fields.bed.gz'))

read_bed(valr_example('6fields.bed.gz'), n_fields = 6)

# result is sorted by chrom and start unless `sort = FALSE`
read_bed(valr_example('3fields.bed.gz'), sort = FALSE)


read_bed12(valr_example('mm9.refGene.bed.gz'))


read_bedgraph(valr_example('test.bg.gz'))


read_narrowpeak(valr_example('sample.narrowPeak.gz'))


read_broadpeak(valr_example('sample.broadPeak.gz'))

# }