downloadUCSCGenome: Download UCSC reference genome

Description Usage Arguments Value Genome Transcriptome Gene annotations Note See Also Examples

View source: R/downloadUCSCGenome.R

Description

Download UCSC reference genome

Usage

1
downloadUCSCGenome(organism, genomeBuild = NULL, outputDir = ".", cache = TRUE)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

genomeBuild

character(1). UCSC genome build assembly name (e.g. "hg38"). If set NULL, defauls to the most recent build available.

outputDir

character(1). Output directory path.

cache

logical(1). Cache URLs locally, using BiocFileCache internally.

Value

Invisible list.

Genome

Transcriptome

Gene annotations

: This directory contains GTF files for the main gene transcript sets where available. They are sourced from the following gene model tables: ncbiRefSeq, refGene, ensGene, knownGene.

Note

Updated 2021-09-03.

See Also

Examples

1
2
## This example is bandwidth intensive.
## > downloadUCSCGenome(organism = "Homo sapiens")

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.