Merge pull request #29 from Durbadal0/testing

Testing

Author: GregFa

Project.toml

@@ -1,6 +1,6 @@
 name = "BigRiverQTL"
 uuid = "8f8ec94a-26d1-428c-aa0e-4e66223094bc"
-authors = ["Gregory Farage, Harper Kolehmainen, Saunak Sen"]
+authors = ["Gregory Farage, Durbadal Ghosh, Harper Kolehmainen, Saunak Sen"]
 version = "0.1.0"
 
 [deps]

README.md

@@ -24,4 +24,103 @@ Pkg.add("BigRiverQTL")
 
 
 ## Contribution
-Contributions to BigRiverQTLPlots.jl are welcome and appreciated. If you'd like to contribute, please fork the repository and make changes as you'd like. If you have any questions or issues, feel free to open an 
+Contributions to BigRiverQTL.jl are welcome and appreciated. If you'd like to contribute, please fork the repository and make changes as you'd like. If you have any questions or issues, feel free to open an 
+
+
+## Examples
+```julia
+using Pkg
+Pkg.activate("../")
+```
+
+
+```julia
+using Revise
+```
+
+
+```julia
+using BigRiverQTLPlots
+using BulkLMM
+using Random, Statistics
+using Plots
+using Helium
+using BigRiverQTL
+using CSV
+using DataFrames
+```
+
+
+```julia
+##############
+# BXD spleen #
+##############
+
+########
+# Data #
+########
+data_dir = joinpath(@__DIR__, "../data/BXD/");
+file = joinpath(data_dir, "bxd.json");
+```
+
+
+```julia
+# Transforming data to a optimised and accessible data type
+data = get_geneticstudydata(file);
+```
+
+
+```julia
+gInfo=data.gmap;
+pInfo=data.phenocov;
+pheno=data.pheno;
+pheno=data.pheno.val;
+geno=data.geno.val[1];
+geno_processed=convert(Array{Float64}, geno);
+```
+
+
+```julia
+#################
+# Preprocessing #
+#################
+traitID = 1112;
+pheno_y = pheno[:, traitID];
+pheno_y2=ones(length(pheno_y));
+pheno_y2[findall(x->x!=nothing,pheno_y)]=pheno_y[findall(x->x!=nothing,pheno_y)];
+```
+
+
+```julia
+###########
+# Kinship #
+###########
+kinship = kinship_gs(geno_processed,.99)
+```
+
+
+```julia
+########
+# Scan #
+########
+
+single_results_perms = scan(
+	pheno_y2,
+	geno_processed,
+	kinship;
+	permutation_test = true,
+	nperms = 1000,
+);
+```
+
+
+```julia
+########
+# Plot #
+########
+
+plot_QTL(single_results_perms, gInfo)
+
+
+```
+[]()

example/Example1.ipynb

@@ -0,0 +1,13 @@
+function gmap2df(gmap::Gmap)
+    v=reduce(vcat,gInfo.marker_name);
+    Mb=reduce(vcat,gInfo.pos);
+    start=0
+    vchr=repeat(["0"],sum(length.(gInfo.marker_name)))
+    for i in 1: eachindex()
+        l_i=length(gInfo.marker_name[i])
+        vchr[start+1:l_i+start] .= gInfo.chr[i]
+        start=start+l_i
+    end
+
+
+end