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update GWAS: fixed data type for 2nd and 3rd column when read mapfile. #156

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Sep 10, 2024
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update GWAS: fixed data type for 2nd and 3rd column when read mapfile. #156

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8bb0c2e
G to G.val
zhaotianjing Apr 3, 2024
797634f
fixed data type when read mapfile
zhaotianjing Sep 10, 2024
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4 changes: 2 additions & 2 deletions src/1.JWAS/src/markers/BayesianAlphabet/MTBayesC0L.jl
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
function MTBayesL!(genotypes,ycorr_array,vare)
MTBayesL!(genotypes.mArray,genotypes.mRinvArray,genotypes.mpRinvm,
ycorr_array,genotypes.α,genotypes.gammaArray,vare,genotypes.G)
ycorr_array,genotypes.α,genotypes.gammaArray,vare,genotypes.G.val)
end

function MTBayesC0!(genotypes,ycorr_array,vare)
MTBayesL!(genotypes.mArray,genotypes.mRinvArray,genotypes.mpRinvm,
ycorr_array,genotypes.α,[1.0],vare,genotypes.G)
ycorr_array,genotypes.α,[1.0],vare,genotypes.G.val)
end

function MTBayesL!(xArray,xRinvArray,xpRinvx,
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6 changes: 3 additions & 3 deletions src/3.GWAS/src/GWAS.jl
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Expand Up @@ -76,7 +76,7 @@ function GWAS(mme,map_file,marker_effects_file::AbstractString...;
end

window_size_bp = map(Int64,parse(Float64,split(window_size)[1])*1_000_000)
mapfile = CSV.read(map_file, DataFrame, header = header, types=Dict(1 => String)) #the 1st column (markerID) must be string
mapfile = CSV.read(map_file, DataFrame, header = header, types=Dict(1 => String, 2 => String, 3 => Int64)) #the 1st column (markerID) must be string
#remove SNPs in mapfile that are not used in Bayesian analysis (e.g., removed in QC)
snpID = mme.M[1].markerID
in_snpID = findall(x -> x ∈ snpID, mapfile[:,1])
Expand All @@ -85,8 +85,8 @@ function GWAS(mme,map_file,marker_effects_file::AbstractString...;
error("Please check the 1st column of the mapfile (i.e., marker ID)")
end

chr = map(string,mapfile[:,2])
pos = map(Int64,mapfile[:,3])
chr = mapfile[:,2]
pos = mapfile[:,3]

window_size_nSNPs = Array{Int64,1}() #save number of markers in ith window for all windows
window_chr = Array{String,1}() #1
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