process_gwas_sumstats: Process GWAS summary statistics and harmonize with LD...

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

Process GWAS summary statistics and harmonize with LD reference

Description

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

Usage

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.

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.