load_GWAS_data {PAST} | R Documentation |
Load GWAS data
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") )
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 |
The association data and the effects data merged into a dataframe with one row for each SNP
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)