annovar: Annotate Genes
In cmcouto-silva/gt: Facilities for essential tasks in R

Description Usage Arguments Details Value Author(s) Examples

Annotate Genes

annovar(
  bim,
  out,
  build = "hg19",
 
    ref_annovar = "~/cmcouto.silva@usp.br/lab_files/datasets/Reference_annotation/annovar"
)

`bim`	Scalar character. Path to Plink bim file.
`out`	Scalar character with desired name for the output file (without extension).
`build`	Scalar character. Build version of the downloaded human database (e.g. hg18 or hg19).
`ref_annovar`	Scalar character. Path to the folder with downloaded ANNOVAR database.

ANNOVAR (annotate_variation.pl) must be installed on the system path.

Tidy text file with chromosome, position, gene and its functional location.

Cainã Max Couto-Silva

## Not run: 
dir.create(annot)
bim <- "path_to_bim_file/file.bim"
out <- "annot/my_annotation" # can be missing, then directory with bim file will be taken

annovar(bim, out, build = "hg19", ref_annovar = "path_to_humandb/")

## End(Not run)