gwas_format: Convert GWAS summary statistics to a standard format

In jean997/sumstatFactors: Genetic Factor Analysis (GFA)

Convert GWAS summary statistics to a standard format

Description

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.

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).

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.

jean997/sumstatFactors documentation built on Jan. 24, 2025, 4:42 a.m.