very useful method that I'm running already for genotyped data, but also wanted to run on VCF files containing imputed data.
When running the command (Julia 1.8.5):
ERROR: MethodError: no method matching isless(::Int64, ::Nothing)
Closest candidates are:
isless(::Integer, ::ForwardDiff.Dual{Ty}) where Ty at ~/.julia/packages/ForwardDiff/QdStj/src/dual.jl:145
isless(::Integer, ::Result) at ~/.julia/packages/NLopt/OIUOZ/src/NLopt.jl:81
isless(::Real, ::Static.StaticInteger{Y}) where Y at ~/.julia/packages/Static/Ldb7F/src/Static.jl:456
...
Stacktrace:
[1] <(x::Int64, y::Nothing)
@ Base ./operators.jl:356
[2] >(x::Nothing, y::Int64)
@ Base ./operators.jl:382
[3] copy_ds!(A::Vector{Union{Missing, Float64}}, reader::VariantCallFormat.Reader; key::String, model::Symbol, impute::Bool, center::Bool, scale::Bool, msg::String, sampleID::Nothing, record_chr::Vector{Any}, record_pos::Vector{Any}, record_ids::Vector{Any}, record_ref::Nothing, record_alt::Nothing)
@ VCFTools ~/.julia/packages/VCFTools/qtvvr/src/convert.jl:702
[4] WARNING: both OrdinalMultinomialModels and Distributions export "cor"; uses of it in module OrdinalGWAS must be qualified
WARNING: both OrdinalMultinomialModels and Distributions export "loglikelihood"; uses of it in module OrdinalGWAS must be qualified
(::OrdinalGWAS.var"#26#32"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLopt.Optimizer, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrame, VariantCallFormat.Reader})(io::IOStream)
@ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:724
[5] makestream(::OrdinalGWAS.var"#26#32"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLopt.Optimizer, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrame, VariantCallFormat.Reader}, ::String, ::Vararg{String})
@ SnpArrays ~/.julia/packages/SnpArrays/60wqu/src/codec.jl:31
[6] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, vcffile::String, nsamples::Int64, vcftype::Symbol; analysistype::String, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1}, snpinds::
Nothing, vcfrowinds::UnitRange{Int64}, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, snpset::Nothing, e::Nothing)
@ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:695
[7] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, geneticfile::String; analysistype::String, geneticformat::String, vcftype::Symbol, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1},
snpinds::Nothing, geneticrowinds::Nothing, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, snpset::Nothing, e::Nothing)
@ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:228
[8] ordinalgwas(nullformula::FormulaTerm{Term, NTuple{12, Term}}, nulldf::DataFrame, geneticfile::String; nullfile::String, link::LogitLink, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, NamedTuple{(:pvalfile, :geneticformat, :vcftype
), Tuple{String, String, Symbol}}})
@ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:134
[9] ordinalgwas(nullformula::FormulaTerm{Term, NTuple{12, Term}}, covfile::String, geneticfile::String; covtype::Nothing, covrowinds::Nothing, kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, NamedTuple{(:pvalfile, :geneticformat, :vcftype), Tuple{String, String, Symbol}}})
@ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:112
[10] top-level scope
@ REPL[11]:1
Going directly to the BGEN file doesn't work, as I don't seem to be able to find the option on how to integrate the .sample file with the .bgen file in OrdinalGWAS