addGenes: Add columns with distance to nearest gene and gene symbol(s)

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

Description

Add columns with distance to nearest gene and gene symbol(s)

Usage

addGenes(query, geneset, genome, cachedir, sync = TRUE)

Arguments

query	Genomic regions to find nearest genes for as a GRanges, data.frame, or data.table with the columns "chr", "start", and "end"
geneset	Select one of "ucsc" for the UCSC Genes (from the knownGene table), "refseq" for RefSeq genes (from the refFlat table), or "ensembl" for the Ensembl genes (from the ensGene table)
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.