bed2gene: Annotate BED file with gene names
In askol-lurie/Bed2GeneRPackage: Annotate BED file with genes

Annotate BED file with gene names based on overlap between the BED interval and coding exons

bed2gene(
  file,
  genes = c(),
  geneFile = "",
  prefix = "",
  outDir = pwd(),
  build = "hg19",
  rmChrM = TRUE
)

`file`	BED file
`genes`	Only output and annotation for intervals that overlap genes in list. Default is an empty vector which results in all genes being output. (optional)
`geneFile`	File containing genes. Only output and annotation for intervals that overlap genes in the file will be output. Alternately, genes can be entered using the gene argument. (optional)
`prefix`	Prefix for output files (optional)
`outDir`	Output directory. If not given results will be printed to pwd(). (optional)
`build`	Build reference for the position coordingates int he BED file (hg19 or hg38)
`rmChrM`	Indicates if mitochondrial genes should be output and annotated (TRUE/FALSE)