Annotate a dataframe containing genomic coordinates with rsids

This function can be used rapidly add rsids to GWAS summary statistics or any other dataframe containing genomic coordinates (eg. chromosome and position). This is a rapid function that does not explicitly account for differences in variants at each position, strand flips, etc.)

Usage

annotate_rsids(
  df,
  dbSNP = SNPlocs.Hsapiens.dbSNP144.GRCh37::SNPlocs.Hsapiens.dbSNP144.GRCh37,
  chrom_col = Chromosome,
  pos_col = Position
)

Arguments

df

Dataframe containing genomic coordinates to annotate with rsid

dbSNP

Bioconductor object containing SNP locations and alleles to be used for annotation (default: SNPlocs.Hsapiens.dbSNP144.GRCh37::SNPlocs.Hsapiens.dbSNP144.GRCh37)

chrom_col

Chromosome column

pos_col

Position column

Value

A dataframe containing the original contents, with an additional rsid column.

Examples

if (FALSE) {
annotate_rsids(sumstats_df)
}