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.

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 x 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 #> # … with 15 more rows
if (FALSE) { # `read_genome` accepts a URL read_genome('https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes') }