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Convert GWAS summary statistics to a standard format

gwas_format.Rd

Format GWAS summary statistics for CAUSE

Usage

gwas_format(
  X,
  snp,
  beta_hat,
  se,
  A1,
  A2,
  chrom,
  pos,
  p_value,
  sample_size,
  allele_freq,
  output_file,
  compute_pval = TRUE
)

Arguments

X

data.frame

snp

Column name containing SNP ID

beta_hat

Column name containing effect estimate

se

Column name containing standard error of beta_hat

A1

Column name containing effect allele

A2

Column name containing other allele

chrom

Chromosome column (optional)

pos

Position column (optional)

p_value

p-value column (optional)

sample_size

Sample size column (optional) or an integer

output_file

File to write out formatted data. If missing formatted data will be returned.

compute_pval

Logical, compute the p-value using a normal approximation if missing? Defaults to TRUE.

Value

A data frame with columns chrom, pos, snp, A1, A2, beta_hat, se, p_value, and sample_size with all SNPs aligned so that A is the effect allele. This is ready to be used with gwas_merge with formatted = TRUE.

Details

This function will try to merge data sets X1 and X2 on the specified columns. Where necessary, it will flip the sign of effects so that the effect allele is the same in both data sets. It will remove variants with ambiguous alleles or where the alleles (G/C or A/T) or with alleles that do not match between data sets (e.g A/G in one data set and A/C in the other). It will not remove variants that are simply strand flipped between the two data sets (e. g. A/C in one data set, T/G in the other).