liftover_gwas: Liftover GWAS positions

In MRCIEU/EbiDataImport: Import EBI Data to OpenGWAS

Liftover GWAS positions

Description

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

MRCIEU/EbiDataImport documentation built on May 9, 2023, 6 a.m.