Process GWAS summary statistics and harmonize with LD reference

Process GWAS summary statistics and adds metadata, including: the index in the bigSNP object of each SNP, and the LD block locus.

process_gwas_sumstats(
  sumstats,
  chr = "chr",
  pos = "pos",
  beta = "beta",
  se = "se",
  a0 = "a0",
  a1 = "a1",
  snp = "snp",
  pval = "pval",
  remove_indels = TRUE,
  LD_Blocks = NULL,
  bigSNP = NULL,
  LD_snp_info = NULL,
  strand_flip = TRUE,
  remove_strand_ambig = TRUE,
  ...
)

Arguments

sumstats: A data frame of GWAS summary statistics.
chr: Name of the chromosome column in summary statistics.
pos: Name of the position column (base pair position).
beta: Name of beta column (if you have Odds Ratio, you will need to transform it to log(Odds Ratio)).
se: Name of the standard error (se) column.
a0: Column name of the reference allele.
a1: Column name of the association/effect allele.
snp: Name of the SNP ID (rsID) column.
pval: Name of the p-value column.
remove_indels: If TRUE, remove indels
LD_Blocks: A data frame of LD blocks with four columns, 'chr', 'start', 'end', and 'locus' (locus ID).
bigSNP: a bigsnpr object attached via bigsnpr::snp_attach() containing the reference genotype panel.
LD_snp_info: a data frame, SNP info in the LD reference, with columns 'chrom', 'id', 'pos', 'alt', 'ref', 'locus'.
strand_flip: Whether to flip signs when reverse complement matches? (default is TRUE).
remove_strand_ambig: Whether to remove ambiguous alleles (A/T and C/G)? (default is TRUE).

Value

A data frame of processed GWAS summary statistics.