Preprocess GWAS z-scores, harmonize GWAS z-scores with LD reference

Source: R/ctwas_preprocess_z_snp.R

Preprocess GWAS z-scores, harmonize GWAS z-scores with LD reference

preprocess_z_snp(
  z_snp,
  snp_map,
  drop_multiallelic = TRUE,
  drop_strand_ambig = TRUE,
  varID_converter_fun = NULL,
  logfile = NULL
)

Arguments

z_snp

A data frame with two columns: "id", "A1", "A2", "z". giving the z scores for snps. "A1" is effect allele. "A2" is the other allele.

snp_map

a list of SNP-to-region map for the reference.

drop_multiallelic

If TRUE, multiallelic variants will be dropped from the summary statistics.

drop_strand_ambig

If TRUE remove strand ambiguous variants (A/T, G/C).

varID_converter_fun

a user defined function to convert GWAS variant IDs to the reference variant format.

logfile

The log filename. If NULL, print log info on screen.

Value

a data frame preprocessed GWAS z-scores