Chromosome & position data to variant RSID

Chromosome & position data to variant RSID

chrpos_to_rsid(
  dt,
  chr_col,
  pos_col,
  ea_col = NULL,
  nea_col = NULL,
  flip = "allow",
  alt_rsids = FALSE,
  build = "b37_dbsnp156",
  dbsnp_dir = genepi.utils::which_dbsnp_directory(),
  parallel_cores = parallel::detectCores(),
  verbose = TRUE
)

Arguments

dt

a data.frame like object, or file path, with at least columns (chrom, pos, ea, nea)

chr_col

a string column name; chromosome position

pos_col

a string column name; base position

ea_col

a string column name; effect allele

nea_col

a string column name; non effect allele

flip

a string, options: "report", "allow", "no_flip"

alt_rsids

a logical, whether to return additional alternate RSIDs

build

a string, options: "b37_dbsnp156", "b38_dbsnp156" (corresponds to the appropriate data directory)

dbsnp_dir

a string file path to the dbSNP .fst file directory - see setup documentation

parallel_cores

an integer, the number of cores/workers to set up the future::multisession with

verbose

a logical, runtime reporting

Value

a data.table with an RSID column (or a list: 1-data.table; 2-list of alternate rsids IDs)