Merge pull request #55 from GregFa/main

added selection samples, marker and remove missing

Author: GregFa

example/example_qtl.ipynb

@@ -127,7 +127,10 @@
     "# We can get the genotype matrix using the following command:\n",
     "geno = reduce(hcat, data.geno.val);\n",
     "# For computing reasons, we need to convert the geno matrix in Float64\n",
-    "geno_processed = convert(Array{Float64}, geno);"
+    "geno_processed = geno .- 1.0 |>\n",
+    "    x -> replace(x, missing => 0.5) |>\n",
+    "\n",
+    "# geno_processed = convert(Matrix{Float64}, geno_processed);\n"
    ]
   },
   {

example/example_qtl.jl

@@ -6,7 +6,7 @@
 #       extension: .jl
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.2
+#       jupytext_version: 1.16.4
 #   kernelspec:
 #     display_name: Julia 1.10.4
 #     language: julia
@@ -62,7 +62,11 @@ pheno = data.pheno.val;
 # We can get the genotype matrix using the following command:
 geno = reduce(hcat, data.geno.val);
 # For computing reasons, we need to convert the geno matrix in Float64
-geno_processed = convert(Array{Float64}, geno);
+geno_processed = geno .- 1.0 |>
+    x -> replace(x, missing => 0.5) |>
+
+# geno_processed = convert(Matrix{Float64}, geno_processed);
+
 # -
 
 # #### Preprocessing

src/BigRiverQTL.jl

@@ -62,8 +62,9 @@ module BigRiverQTL
     ######
     # IO #
     ######
-    include("io/io_utils.jl")
+    include("io/io_helpers.jl")
     export get_control_file, encode_genotype
+
     include("io/export_to_type.jl")
     export get_geneticstudydata
     export get_gmap, get_alleles, get_chromosome, get_crossinfo, get_crosstype 
@@ -73,7 +74,7 @@ module BigRiverQTL
     #########
     # Plots #
     #########
-    include("plots/plots_utils.jl")
+    include("plots/plots_helpers.jl")
     export gmap2df, pmap2df
 
     include("plots/plots_qtl.jl")
@@ -85,4 +86,10 @@ module BigRiverQTL
     include("plots/plots_eqtl.jl")
     export plot_eQTL 
 
+    #########
+    # Utils #
+    #########
+    include("utils/wrangling_utils.jl")
+    export get_geno_completecases, summary_missing, select_sample, select_marker
+    
 end