match_gwas_bigsnp: Match alleles between GWAS summary statistics and bigSNP...

In kevinlkx/Mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Match alleles between GWAS summary statistics and bigSNP reference panel.

Description

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).

Usage

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.

kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.