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Read GWAS summary statistics

Source: R/ctwas_utils.R
read_gwas.Rd

Read GWAS summary statistics

Usage

read_gwas(
  gwas,
  id = "rsid",
  A1 = "ALT",
  A2 = "REF",
  z = "Z",
  beta = "ES",
  se = "SE"
)

Arguments

gwas

A data frame of GWAS summary statistics.

id

Column name of the variant IDs.

A1

Column name of the alternative alleles.

A2

Column name of the reference alleles.

z

Column name of z-scores.

beta

Column name of effect sizes. If z is not available, compute z from beta and se.

se

Column name of the standard errors.

Value

A data frame of processed GWAS summary statistics.