Read genome files.

Genome files (UCSC "chromSize" files) contain chromosome name and size information. These sizes are used by downstream functions to identify computed intervals that have coordinates outside of the genome bounds.

Usage

read_genome(path)

Arguments

path

containing chrom/contig names and sizes, one-pair-per-line, tab-delimited

Value

genome_df, sorted by size

Note

URLs to genome files can also be used.

See also

Other read functions: read_bed(), read_vcf()

Examples

read_genome(valr_example("hg19.chrom.sizes.gz"))
#> # A tibble: 25 × 2
#>    chrom      size
#>    <chr>     <dbl>
#>  1 chr1  249250621
#>  2 chr2  243199373
#>  3 chr3  198022430
#>  4 chr4  191154276
#>  5 chr5  180915260
#>  6 chr6  171115067
#>  7 chr7  159138663
#>  8 chrX  155270560
#>  9 chr8  146364022
#> 10 chr9  141213431
#> # ℹ 15 more rows

if (FALSE) { # \dontrun{
# `read_genome` accepts a URL
read_genome("https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes")
} # }