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Convert CHR:BP to rsID (not recommended)

add_rsid.Rd

This function takes a dataframe that must include columns 'CHR' and 'BP', and it appends the corresponding rsID by querying the SNPlocs.Hsapiens.dbSNP155.GRCh37 database. The function returns a dataframe with the rsIDs included.

Usage

add_rsid(dat, ref = "GRCh37")

Arguments

dat

  • "GRCh38" for GRCh38 Ref panel

ref

str indicating ref version.

  • "GRCh37" for GRCh37 Ref panel

Value

A dataframe with an additional 'RefSNP_id' column which contains the rsIDs.

Examples

if (FALSE) { # \dontrun{
pacman::p_load(data.table, BSgenome, leo.gwas)
library("SNPlocs.Hsapiens.dbSNP155.GRCh37") # for GRCh37
library("SNPlocs.Hsapiens.dbSNP155.GRCh38") # for GRCh38
df <- data.frame(
  CHR = c(1, 1),
  BP = c(15211, 15820)
)
result <- add_rsid(df); result
} # }