clean_sumstats: Cleans summary statistics

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

Cleans summary statistics

Description

It will extract the required columns from summary statistics, check chromosomes, remove X, Y chromosomes, compute z-scores, convert alleles to upper case, remove indels, and sort by chromosome and position.

Usage

clean_sumstats(
  sumstats,
  chr = "chr",
  pos = "pos",
  beta = "beta",
  se = "se",
  a0 = "a0",
  a1 = "a1",
  snp = "snp",
  pval = "pval",
  remove_indels = TRUE
)

Arguments

sumstats	A data frame of GWAS summary statistics. It is required to have the following columns: chr, position, beta, se, a0, a1, SNP ID (rs), p-value.
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.

Value

A data frame of cleaned summary statistics, sort by chromosome and position.

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