Augment a data.frame with information from dbSNP — repair_ids • tidyGWAS

Augment a data.frame with information from dbSNP

Usage

repair_ids(
  tbl,
  repair = c("rsid", "pos"),
  build = c("NA", "37", "38"),
  dbsnp_path
)

Arguments

tbl: a dplyr::tibble() with columns CHR, POS, EffectAllele, OtherAllele or RSID, EffectAllele, OtherAllele2.
repair: "rsid" to repair RSID, "pos" to repair CHR and POS
build: used if repair = "rsid" to specify genome build
dbsnp_path: path to the directory containing the dbSNP dataset

Value

a dplyr::tibble() with added columns CHR, POS_37, POS_38 RSID, REF_37, ALT_37, REF_38, ALT_38, no_dbsnp_entry, incompat_alleles

Examples

if (FALSE) { # \dontrun{
repair_ids(gwas_sumstats, repair = "rsid", build = "38", dbsnp_path = "/path/to/dbsnp")
} # }