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added selection samples, marker and remove missing #55

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Merged
merged 6 commits into from
Aug 22, 2024
Merged

added selection samples, marker and remove missing #55

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a4b58be
used geno_transposed value in get_geno
GregFa Aug 19, 2024
c6959cc
corrected code usng transposed geno
GregFa Aug 19, 2024
0aed57f
changed name plots_utils to plots_helpers
GregFa Aug 20, 2024
3a1ce70
rename io_utils to io_helpers
GregFa Aug 20, 2024
6e5ed83
added wrangling_utils
GregFa Aug 21, 2024
1b40225
added selection samples and marker
GregFa Aug 21, 2024
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5 changes: 4 additions & 1 deletion example/example_qtl.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
},
{
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8 changes: 6 additions & 2 deletions example/example_qtl.jl
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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11 changes: 9 additions & 2 deletions src/BigRiverQTL.jl
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Expand Up @@ -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
Expand All @@ -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")
Expand All @@ -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
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