get.chrom.length: Get Chromosome Length

In GRIN2: Genomic Random Interval (GRIN)

Get Chromosome Length

Description

Retrieve chromosome size data from chr.info txt files available on the UCSC genome browser based on the user specified genome assembly.

Usage

get.chrom.length(genome.assembly)

Arguments

genome.assembly

User can specify one of four supported genome assemblies that include "Human_GRCh38", "Human_GRCh37", "Mouse_HGCm39" and "Mouse_HGCm38".

Details

Based on the genome assembly specified by the user, the function will directly retrieve chromosome size data from chr.info txt file available on the UCSC genome browser.

Value

A data table with the following two columns:

chrom	column has the chromosome number denoted as 1, 2, X, Y, etc..
size	column has the chromosome size in base pairs.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

See Also

circlize::read.chromInfo()

Examples

# To retreive chromosome size data for hg19 genome assembly:
hg19.chrom.size=get.chrom.length("Human_GRCh37")
# "Human_GRCh38" can be used to retreive chromosome size data for hg38 genome assembly.

GRIN2 documentation built on April 4, 2025, 1:41 a.m.