load_GWAS_data: Load GWAS data

In PAST: Pathway Association Study Tool (PAST)

Description

Load GWAS data

Usage

load_GWAS_data(
  association_file,
  effects_file,
  association_columns = c("Trait", "Marker", "Locus", "Site", "p", "marker_R2"),
  effects_columns = c("Trait", "Marker", "Locus", "Site", "Effect")
)

Arguments

association_file	The association file
effects_file	The effects file
association_columns	The names of the columns in your association data for Trait, Marker, Chromosome, Site, F, p, and marker_Rsquared
effects_columns	The names of the columns in your effects data for Trait, Marker, Chromosome, Site, and effect

Value

The association data and the effects data merged into a dataframe with one row for each SNP

Examples

demo_association_file = system.file("extdata", "association.txt.xz",
  package = "PAST", mustWork = TRUE)
demo_effects_file = system.file("extdata", "effects.txt.xz",
  package = "PAST", mustWork = TRUE)
gwas_data <- load_GWAS_data(demo_association_file, demo_effects_file)

PAST documentation built on Nov. 8, 2020, 8:31 p.m.