read_bed | R Documentation |
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.
read_bed(
filename,
col_types = bed12_coltypes,
sort = TRUE,
...,
n_fields = NULL
)
read_bed12(filename, ...)
read_bedgraph(filename, ...)
read_narrowpeak(filename, ...)
read_broadpeak(filename, ...)
filename |
file or URL |
col_types |
column type spec for |
sort |
sort the tbl by chrom and start |
... |
options to pass to |
n_fields |
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
ivl_df
Other read functions:
read_genome()
,
read_vcf()
# 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"))
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