read_bed {valr}

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,
  col_types = bed12_coltypes,
  sort = TRUE,
  ...,
  n_fields = NULL
)

read_bed12(filename, ...)

read_bedgraph(filename, ...)

read_narrowpeak(filename, ...)

read_broadpeak(filename, ...)

Arguments

filename

file or URL

col_types

column type spec for readr::read_tsv()

sort

sort the tbl by chrom and start

...

options to pass to readr::read_tsv()

n_fields

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

Value

ivl_df

See Also

Other read functions: read_genome(), read_vcf()

Examples

# read_bed assumes 3 field BED format.
read_bed(valr_example("3fields.bed.gz"))

# 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"))