load_gemma_gwas: Load a GEMMA association results file.

In nwvankuren/gwplotting: Utilities for plotting statistics from genome-wide analyses

Load a GEMMA association results file.

Description

This function will read a (possibly gzipped) GEMMA results file (.assoc.txt) and return a tibble containing just the scaffold, position, and statistic.

Usage

load_gemma_gwas(file, pval = "p_wald")

Arguments

file	GEMMA file (.assoc.txt). Can be gzipped.
pval	Statistic column to read. This must match the column name exactly and can be one of the following: p_wald, p_lrt, or p_score.

Value

A three-column tibble containing scaffold, position, and stat

Examples

a <- system.file("extdata", "test.gemma_gwas.txt.gz",
                 package = "gwplotting")

b <- load_gemma_gwas( a, pval = 'p_wald' )
b

nwvankuren/gwplotting documentation built on July 5, 2024, 4:24 p.m.