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
![[Deprecated]](figures/lifecycle-deprecated.svg)
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
See also
Other read functions:
read_genome(),
read_vcf()
Examples
# read_bed assumes 3 field BED format.
read_bed(valr_example("3fields.bed.gz"))
#> # A tibble: 10 × 3
#> chrom start end
#> <chr> <int> <int>
#> 1 chr1 11873 14409
#> 2 chr1 14361 19759
#> 3 chr1 14406 29370
#> 4 chr1 34610 36081
#> 5 chr1 69090 70008
#> 6 chr1 134772 140566
#> 7 chr1 321083 321115
#> 8 chr1 321145 321207
#> 9 chr1 322036 326938
#> 10 chr1 327545 328439
# result is sorted by chrom and start unless `sort = FALSE`
read_bed(valr_example("3fields.bed.gz"), sort = FALSE)
#> # A tibble: 10 × 3
#> chrom start end
#> <chr> <int> <int>
#> 1 chr1 11873 14409
#> 2 chr1 14361 19759
#> 3 chr1 14406 29370
#> 4 chr1 34610 36081
#> 5 chr1 69090 70008
#> 6 chr1 134772 140566
#> 7 chr1 321083 321115
#> 8 chr1 321145 321207
#> 9 chr1 322036 326938
#> 10 chr1 327545 328439
read_bed12(valr_example("mm9.refGene.bed.gz"))
#> # A tibble: 100 × 12
#> chrom start end name score strand cds_start cds_end item_rgb exon_count
#> <chr> <int> <int> <chr> <chr> <chr> <int> <int> <chr> <int>
#> 1 chr1 3204562 3.66e6 NM_0… 0 - 3206102 3661429 0 3
#> 2 chr1 4280926 4.40e6 NM_0… 0 - 4283061 4399268 0 4
#> 3 chr1 4847774 4.89e6 NM_0… 0 + 4847994 4886445 0 10
#> 4 chr1 4847774 4.89e6 NM_0… 0 + 4847994 4886445 0 10
#> 5 chr1 4848408 4.89e6 NM_0… 0 + 4848488 4886445 0 10
#> 6 chr1 4899656 5.01e6 NM_0… 0 - 4900554 4914046 0 5
#> 7 chr1 4899656 5.01e6 NM_0… 0 - 4900554 5009460 0 5
#> 8 chr1 4899656 5.06e6 NM_0… 0 - 4900554 5060258 0 6
#> 9 chr1 5073166 5.15e6 NM_0… 0 + 5074531 5152246 0 13
#> 10 chr1 5073166 5.15e6 NM_1… 0 + 5074531 5152246 0 14
#> # ℹ 90 more rows
#> # ℹ 2 more variables: exon_sizes <chr>, exon_starts <chr>
read_bedgraph(valr_example("test.bg.gz"))
#> # A tibble: 4 × 4
#> chrom start end value
#> <chr> <int> <int> <dbl>
#> 1 chr19 49302000 49302300 -1
#> 2 chr19 49302300 49302600 -0.75
#> 3 chr19 49302600 49302900 -0.5
#> 4 chr19 49302900 49303200 -0.25
read_narrowpeak(valr_example("sample.narrowPeak.gz"))
#> # A tibble: 570 × 10
#> chrom start end name score strand signal pvalue qvalue peak
#> <chr> <int> <int> <chr> <int> <chr> <dbl> <dbl> <dbl> <int>
#> 1 chr22 17372940 17373090 . 0 . 4 4.63 -1 -1
#> 2 chr22 17392200 17392350 . 0 . 5 4.67 -1 -1
#> 3 chr22 17398400 17398550 . 0 . 10 11.6 -1 -1
#> 4 chr22 17539180 17539330 . 0 . 21 30.9 -1 -1
#> 5 chr22 17652440 17652590 . 0 . 6 5.35 -1 -1
#> 6 chr22 17652780 17652930 . 0 . 12 12.5 -1 -1
#> 7 chr22 17980800 17980950 . 0 . 12 12.6 -1 -1
#> 8 chr22 18038260 18038410 . 0 . 29 36.0 -1 -1
#> 9 chr22 18225280 18225430 . 0 . 21 25.0 -1 -1
#> 10 chr22 18268020 18268170 . 0 . 14 13.0 -1 -1
#> # ℹ 560 more rows
read_broadpeak(valr_example("sample.broadPeak.gz"))
#> # A tibble: 1,181 × 9
#> chrom start end name score strand signal pvalue qvalue
#> <chr> <int> <int> <chr> <int> <chr> <dbl> <dbl> <dbl>
#> 1 chr22 16847903 16848440 . 503 . 10.5 2.5 -1
#> 2 chr22 16849452 16851326 . 483 . 9.81 15.7 -1
#> 3 chr22 16849955 16850086 . 1000 . 32.4 4.2 -1
#> 4 chr22 16850694 16850924 . 831 . 22.5 4.9 -1
#> 5 chr22 16852964 16853782 . 499 . 10.4 6.2 -1
#> 6 chr22 16855065 16855803 . 477 . 9.58 3.9 -1
#> 7 chr22 16855944 16856974 . 491 . 10.1 8.5 -1
#> 8 chr22 16857425 16857958 . 505 . 10.6 2.5 -1
#> 9 chr22 16858284 16858824 . 549 . 12.2 4.5 -1
#> 10 chr22 16859972 16862024 . 404 . 6.89 9.3 -1
#> # ℹ 1,171 more rows