loadChr: Load downloaded chromosome into a GenomicRanges object

In jeffbhasin/genomesyncr: genomesyncr: Download, Synchronize, and Parse UCSC Genome Browser Tables from R

Description

After downloading the FASTA for a genome using syncFasta, this function loads a given chromosome only into a DNAStringSet object.

Usage

  loadChr(genome, chr, local)

Arguments

genome	The UCSC string specific to the genome to be downloaded (e.g. "hg19", "hg19", "mm10", etc)
chr	The string specific to the chromosome to load (e.g. "chr1", "chr22", "chr_M", "chr1_random", etc)
local	The root of a local directory where all files downloaded from UCSC are stored

Value

A DNAStringSet object with one sequence for the chromosome from UCSC's FASTA release for the given genome.

jeffbhasin/genomesyncr documentation built on May 19, 2019, 1:45 a.m.