Merge pull request #53 from GregFa/main

Fixed test and updated struct functions
senresearch · Aug 16, 2024 · e6b7d1c · e6b7d1c
2 parents 782ce16 + c0d9c28
commit e6b7d1c
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Showing 10 changed files with 706 additions and 529 deletions.
diff --git a/Project.toml b/Project.toml
@@ -29,7 +29,8 @@ julia = "1"
 
 [extras]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["DelimitedFiles", "Test"]
+test = ["DelimitedFiles", "Plots", "Test"]
diff --git a/src/BigRiverQTL.jl b/src/BigRiverQTL.jl
@@ -7,6 +7,7 @@ module BigRiverQTL
 
     using Reexport
     @reexport import BigRiverQTLPlots: plot_QTL, plot_eQTL, plot_manhattan
+    @reexport import BulkLMM: scan
 
 
     ########
@@ -54,15 +55,20 @@ module BigRiverQTL
     # Structure #
     #############
     include("struct/datastructure.jl")
-    export Gmap, Alleles, CrossType, GenoType, GenoTranspose,Geno, Pmap, Pheno, Phenocov, IsFemale, IsXChar,  CrossInfo
+    export Gmap, Alleles, CrossType, GenoType, GenoTranspose, Geno, Pmap
+    export Pheno, Phenocov, IsFemale, IsXChar, CrossInfo
     export GeneticStudyData
 
     ######
     # IO #
     ######
     include("io/io_utils.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 
+    export get_geno, get_genotype, get_genotranspose, get_pmap
+    export get_phenocovar, get_pheno, get_isxchar
 
     #########
     # Plots #
@@ -76,7 +82,6 @@ module BigRiverQTL
     include("plots/plots_manhattan.jl")
     export plot_manhattan
 
-
     include("plots/plots_eqtl.jl")
     export plot_eQTL