Match alleles between GWAS summary statistics and bigSNP reference panel.

Source: R/harmonization.R

Match alleles between summary statistics and SNP information in the bigSNP reference panel using the bigsnpr::snp_match() function. Match by ("chr", "a0", "a1") and ("pos" or "rsid"), accounting for possible strand flips and reverse reference alleles (opposite effects).

match_gwas_bigsnp(
  sumstats,
  bigSNP,
  strand_flip = TRUE,
  match.min.prop = 0.1,
  ...
)

Arguments

sumstats

A data frame of GWAS summary statistics, with columns "chr", "pos", "a0", "a1" and "beta".

bigSNP

a bigsnpr object attached via bigsnpr::snp_attach() containing the reference genotype panel.

strand_flip

Whether to try to flip strand? (default is TRUE). If so, ambiguous alleles A/T and C/G are removed.

match.min.prop

Minimum proportion of variants in the smallest data to be matched, otherwise stops with an error. Default: 10%

Value

A data frame with matched summary statistics. Values in column "beta" are multiplied by -1 for variants with alleles reversed (i.e. swapped). New variable "ss_index" returns the corresponding row indices of the sumstats, and "bigSNP_index" corresponding to the indices of the bigSNP.