getGenes: Load table of gene ranges via UCSC Genome Browser tables

In jeffbhasin/goldmine: goldmine: Genomic context annotation for any set of genomic ranges using UCSC Genome Browser tables

Description

Load table of gene ranges via UCSC Genome Browser tables

Usage

getGenes(geneset = "ucsc", gencodetable = NULL, genome, cachedir = NULL,
  sync = TRUE)

Arguments

geneset	Select one of "ucsc" for the UCSC Genes (from the knownGene table), "refseq" for RefSeq genes (from the refFlat table), "gencode" for GENCODE genes, or "ensembl" for the Ensembl genes (from the ensGene table)
gencodetable	Only needed if geneset="gencode". Provide the name of the UCSC table that contains the GENCODE genes of interest. There are multiple builds and subsets. Find the GENCODE table names for a given geome listed under "Genes and Gene Predictions" at http://genome.ucsc.edu/cgi-bin/hgTables (for example, "wgEncodeGencodeCompV24lift37" is one available for "hg19")
genome	UCSC genome name to use (e.g. hg19, mm10)
cachedir	Path where cached UCSC tables are stores
sync	If TRUE, then check if newer versions of UCSC tables are available and download them if so. If FALSE, skip this check. Can be used to freeze data versions in an analysis-specific cachedir for reproducibility.

jeffbhasin/goldmine documentation built on Nov. 13, 2019, 9:11 a.m.