read_genome: Read genome files.

In jayhesselberth/valr: Genome Interval Arithmetic

Read genome files.

Description

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"))

## Not run: 
# `read_genome` accepts a URL
read_genome("https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes")

## End(Not run)

jayhesselberth/valr documentation built on April 24, 2024, 7:15 a.m.