From 5c74aebc23b049d781cbcae7b76b98eb0bd68826 Mon Sep 17 00:00:00 2001 From: qtlchengadmin Date: Wed, 21 Jul 2021 12:05:05 -0700 Subject: [PATCH] update GWAS for window size --- src/3.GWAS/src/GWAS.jl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/3.GWAS/src/GWAS.jl b/src/3.GWAS/src/GWAS.jl index 4192cc84..9aeea79d 100644 --- a/src/3.GWAS/src/GWAS.jl +++ b/src/3.GWAS/src/GWAS.jl @@ -66,9 +66,10 @@ function GWAS(mme,map_file,marker_effects_file::AbstractString...; if map_file == false && typeof(window_size) <: Integer println("The map file is not provided. A fake map file is generated with $window_size markers in each 1 Mb window.") nmarkers=length(readdlm(marker_effects_file[1],',',header=true)[2]) - mapfile = DataFrame(markerID=1:nmarkers, + positions = + mapfile = DataFrame(markerID =1:nmarkers, chromosome=fill(1,nmarkers), - position=1:10_000:nmarkers*10_000) + position =Int.(floor.(1:(1_000_000/window_size):nmarkers*(1_000_000/window_size)))) CSV.write("mapfile.temp",mapfile) map_file, window_size = "mapfile.temp", "1 Mb" end