Get RSIDS from SNP coordinates — coords_to_rsids • echodata

Get RSIDS from SNP coordinates using Bioconductor genome references.

Usage

coords_to_rsids(
  dat,
  genome_build = "hg19",
  drop_unannotated = TRUE,
  drop_duplicates = TRUE,
  SNPname = "SNP",
  verbose = TRUE
)

Arguments

dat: data.table or data.frame with SNP positions in the columns CHR and POS. Extra columns are allowed.
genome_build: Which genome build dat is in (e.g. "hg19" or "hg38").
drop_unannotated: Drop SNPs that RSIDs couldn't be found for.
drop_duplicates: Drop any duplicate SNPs rows.
SNPname: Name of the new column with RSIDs.
verbose: Print messages.

Value

data.table with new columns for RSIDs.

Examples

# \donttest{
dat <- echodata::BST1[seq(5),]
data.table::setnames(dat,"SNP","SNP_old")
dat_annot <- coords_to_rsids(dat = dat)
#> Searching for RSIDs using: hg19
#> Loading required namespace: SNPlocs.Hsapiens.dbSNP144.GRCh37
#> Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
#> 5 / 5 SNPs annotated with RSIDs.
# }