Liftover GWAS positions — liftover

Determine GWAS build and liftover to required build

Usage

liftover_gwas(
  dat,
  build = c(37, 38, 36),
  to = 37,
  chr_col = "chr",
  pos_col = "pos",
  snp_col = "snp",
  ea_col = "ea",
  oa_col = "oa",
  build_fallback = "position"
)

Arguments

dat: Data frame with chr, pos, snp name, effect allele, non-effect allele columns
build: The possible builds to check data against Default = c(37,38,26)
to: Which build to lift over to. Default=37
chr_col: Name of chromosome column name. Required
pos_col: Name of position column name. Required
snp_col: Name of SNP column name. Optional. Uses less certain method of matching if not available
ea_col: Name of effect allele column name. Optional. Might lead to duplicated rows if not presented
oa_col: Name of other allele column name. Optional. Might lead to duplicated rows if not presented
build_fallback: Whether to try "position" (fast) or "biomart" (more accurate if you have rsids) based approaches instead

Value

Data frame