update GWAS for window size

reworkhow · Jul 21, 2021 · 5c74aeb · 5c74aeb
1 parent 824230a
commit 5c74aeb
Showing 1 changed file with 3 additions and 2 deletions.
diff --git 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