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Read GEMMA association results

Source: R/read-gemma.R
read_gemma.Rd

Read GEMMA association results

Usage

read_gemma(file, p_column = "p_wald", ...)

Arguments

file

Path to a GEMMA .assoc.txt file.

p_column

Which p-value column to use: "p_wald", "p_lrt", or "p_score".

...

Additional arguments passed to data.table::fread().

Value

A gwas_data object.

Examples

f <- system.file("extdata", "example_gemma.assoc.txt", package = "ggwas")
gwas <- read_gemma(f)
#> Read 4 variants from example_gemma.assoc.txt
gwas
#> A gwas_data object: 4 variants across 3 chromosomes
#>   Min p-value: 5.20e-08
#>   Lambda GC:   3.171
#>   Columns:     CHR, BP, SNP, P, BETA, SE, A1, A2, AF, n_miss, logl_H1, l_remle