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improve readgenotypes before line "isGRM = false"
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@zhaotianjing
zhaotianjing committed Feb 21, 2024
1 parent f7ceaeb commit 87b3233
Showing 1 changed file with 45 additions and 35 deletions.
80 changes: 45 additions & 35 deletions src/1.JWAS/src/markers/readgenotypes.jl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
"""
DEPRECATED!! Please use get_genotypes()
add_genotypes(mme::MME,M::Union{AbstractString,Array{Float64,2},Array{Float32,2},Array{Any,2},DataFrames.DataFrame},G=false;
header=false,rowID=false,separator=',',
center=true,G_is_marker_variance=false,df=4)
Expand Down Expand Up @@ -51,11 +53,19 @@ end
#1)load genotypes from a text file (1st column: individual IDs; 1st row: marker IDs (optional))
#2)load genotypes from Array or DataFrames (no individual IDs; no marker IDs (header))
"""
get_genotypes(file::Union{AbstractString,Array{Float64,2},Array{Float32,2},Array{Any,2},DataFrames.DataFrame},G=false;
separator=',',header=true,rowID=false,
center=true,quality_control=false,
method = "RR-BLUP",Pi = 0.0,estimatePi = true,estimate_scale=false,estimate_variance=true,
G_is_marker_variance = false,df = 4.0)
get_genotypes(file::Union{AbstractString,Array{Float64,2},Array{Float32,2},Array{Int64,2}, Array{Int32,2}, Array{Any,2}, DataFrames.DataFrame}, G = false;
## method:
method = "BayesC",Pi = 0.0,estimatePi = true,
## variance:
G_is_marker_variance = false, df = 4.0,
estimate_variance=true, estimate_scale=false,
constraint = false, #for multi-trait only, constraint=true means no genetic covariance among traits
## format:
separator=',',header=true,rowID=false,
## quality control:
quality_control=true, MAF = 0.01, missing_value = 9.0,
## others:
center=true,starting_value=false)
* Get marker informtion from a genotype file/matrix. This file needs to be column-wise sorted by marker positions.
* If a text file is provided, the file format should be:
```
Expand All @@ -82,62 +92,62 @@ end
* Scale parameter for prior of marker effect variance is estimated if `estimate_scale` = true, defaulting to `false`.
"""
function get_genotypes(file::Union{AbstractString,Array{Float64,2},Array{Float32,2},Array{Any,2},DataFrames.DataFrame},G=false;
function get_genotypes(file::Union{AbstractString,Array{Float64,2},Array{Float32,2},Array{Int64,2}, Array{Int32,2}, Array{Any,2}, DataFrames.DataFrame}, G = false;
## method:
method = "BayesC",Pi = 0.0,estimatePi = true,
method = "BayesC", Pi = 0.0, estimatePi = true,
## variance:
G_is_marker_variance = false, df = 4.0,
estimate_variance=true, estimate_scale=false,
estimate_variance = true, estimate_scale = false,
constraint = false, #for multi-trait only, constraint=true means no genetic covariance among traits
## format:
separator=',',header=true,rowID=false,
separator = ',', header = true,
## quality control:
quality_control=true, MAF = 0.01, missing_value = 9.0,
quality_control = true, MAF = 0.01, missing_value = 9.0,
## others:
center=true,starting_value=false)
center = true, starting_value = false)
#Read the genotype file
if typeof(file) <: AbstractString
printstyled("The delimiterd in ",split(file,['/','\\'])[end]," is \'",separator,"\'. ",bold=false,color=:green)
printstyled("The header (marker IDs) is ",(header ? "provided" : "not provided")," in ",split(file,['/','\\'])[end],".\n",bold=false,color=:green)
if typeof(file) <: AbstractString #string (path to a file)
#print info about the file format
printstyled("The delimiter in ", split(file, ['/', '\\'])[end], " is \'", separator, "\'. ", bold=false, color=:green)
printstyled("The header (marker IDs) is ", (header ? "provided" : "not provided"), " in ", split(file, ['/', '\\'])[end], ".\n", bold=false, color=:green)
#get marker IDs
myfile = open(file)
row1 = split(readline(myfile),[separator,'\n'],keepempty=false)
if header==true
markerID=string.(row1[2:end]) #skip header
row1 = split(readline(myfile), [separator, '\n'], keepempty=false) #read the first row
if header == true
markerID = string.(row1[2:end]) #extracts marker IDs from row1
else
markerID=string.(1:length(row1[2:end]))
markerID = string.(1:length(row1[2:end])) #generate default marker IDs if no header
end
#set type for each column
ncol= length(row1)
etv = Array{DataType}(undef,ncol)
fill!(etv,Float64)
etv[1]=String
ncol = length(row1)
etv = Array{DataType}(undef, ncol)
fill!(etv, Float32)
etv[1] = String #individual ID
close(myfile)
#read a large genotype file
data = CSV.read(file,DataFrame,types=etv,delim = separator,header=false,skipto=(header==true ? 2 : 1))
obsID = map(string,data[!,1])
genotypes = map(Float32,Matrix(data[!,2:end]))
genotypes = Matrix{Float32}(data[!,2:end]) #memory usage is doubled here; cannot use readdlm because 1st column is string
#clean memory
data = nothing
GC.gc()
elseif typeof(file) == DataFrames.DataFrame #Datafarme
println("The first column in the dataframe should be individual IDs.")
println("The data type of markers should be Number.")
println("The remaining columns are markers with the data type Number.")
if header == true
markerID = names(file)[2:end]
else
markerID = string.(1:(size(file,2)-1))
printstyled("The marker IDs are set to 1,2,...,#markers\n",bold=true)
end
obsID = map(string,file[!,1])
genotypes = map(Float32,Matrix(file[!,2:end]))
elseif typeof(file) <: Union{Array{Float64,2},Array{Float32,2},Array{Any,2}} #Array
if length(header) != (size(file,2)+1)
header = ["id"; string.(1:size(file,2))]
printstyled("The marker IDs are set to 1,2,...,#markers\n",bold=true)
end
if length(rowID) != size(file,1)
rowID = string.(1:size(file,1))
printstyled("The individual IDs is set to 1,2,...,#observations\n",bold=true)
end
markerID = string.(header[2:end])
obsID = map(string,rowID)
elseif typeof(file) <: Union{Array{Float64,2}, Array{Float32,2}, Array{Int64,2}, Array{Int32,2}, Array{Any,2}} #Array (Matrix)
println("The input data is a genotype matrix, without individual IDs.")
markerID = string.(1:size(file,2))
printstyled("The marker IDs are set to 1,2,...,#markers\n",bold=true)
obsID = map(string,string.(1:size(file,1)))
printstyled("The individual IDs is set to 1,2,...,#observations\n",bold=true)
genotypes = map(Float32,convert(Matrix,file))
else
error("The data type is not supported.")
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