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scan function "weights" data type issue #101

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jb621-star opened this issue Jun 12, 2024 · 0 comments
Open

scan function "weights" data type issue #101

jb621-star opened this issue Jun 12, 2024 · 0 comments

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@jb621-star
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I have the following toy example to use with the "weights" option within the "scan" function:

y = rand(100, 1) # Example phenotype matrix
g = rand(100, 10) # Example genotype matrix
covar = rand(100, 5) # Example covariate matrix
K = rand(100, 100) # Example kinship matrix
weights = rand(100) # Example weights vector

# Call scan function
result = scan(y, g, covar, K; weights=weights, output_pvals = true);
println(result)

From scan I get the following error message:

ERROR: MethodError: no method matching isless(::ComplexF64, ::Float64)

Closest candidates are:
  isless(::T, ::T) where T<:Union{Float16, Float32, Float64}
   @ Base float.jl:547
  isless(::Union{StatsBase.PValue, StatsBase.TestStat}, ::AbstractFloat)
   @ StatsBase ~/.julia/packages/StatsBase/WLz8A/src/statmodels.jl:99
  isless(::Union{StatsBase.PValue, StatsBase.TestStat}, ::Real)
   @ StatsBase ~/.julia/packages/StatsBase/WLz8A/src/statmodels.jl:90
  ...

Stacktrace:
  [1] <(x::ComplexF64, y::Float64)
    @ Base ./operators.jl:343
  [2] _broadcast_getindex_evalf
    @ ./broadcast.jl:683 [inlined]
  [3] _broadcast_getindex
    @ ./broadcast.jl:656 [inlined]
  [4] getindex
    @ ./broadcast.jl:610 [inlined]
  [5] copy
    @ ./broadcast.jl:912 [inlined]
  [6] materialize
    @ ./broadcast.jl:873 [inlined]
  [7] transform_rotation(y::Matrix{Float64}, g::Matrix{Float64}, K::Matrix{Float64}; addIntercept::Bool, decomp_scheme::String)
    @ BulkLMM ~/.julia/packages/BulkLMM/bdDFk/src/transform_helpers.jl:27
  [8] transform_rotation
    @ ~/.julia/packages/BulkLMM/bdDFk/src/transform_helpers.jl:1 [inlined]
  [9] scan_null(y::Matrix{Float64}, g::Matrix{Float64}, covar::Matrix{Float64}, K::Matrix{Float64}, prior::Vector{Float64}, addIntercept::Bool; reml::Bool, method::String, optim_interval::Int64, decomp_scheme::String, output_pvals::Bool, chisq_df::Int64)
    @ BulkLMM ~/.julia/packages/BulkLMM/bdDFk/src/scan.jl:323
 [10] scan_null
    @ ~/.julia/packages/BulkLMM/bdDFk/src/scan.jl:310 [inlined]
 [11] scan(y::Matrix{Float64}, g::Matrix{Float64}, covar::Matrix{Float64}, K::Matrix{Float64}; weights::Missing, prior_variance::Float64, prior_sample_size::Float64, addIntercept::Bool, reml::Bool, assumption::String, method::String, optim_interval::Int64, permutation_test::Bool, nperms::Int64, rndseed::Int64, profileLL::Bool, markerID::Int64, h2_grid::Vector{Float64}, decomp_scheme::String, output_pvals::Bool, chisq_df::Int64)
    @ BulkLMM ~/.julia/packages/BulkLMM/bdDFk/src/scan.jl:236
 [12] scan
    @ ~/.julia/packages/BulkLMM/bdDFk/src/scan.jl:182 [inlined]
 [13] scan(y::Matrix{Float64}, g::Matrix{Float64}, covar::Matrix{Float64}, K::Matrix{Float64}; weights::Vector{Float64}, prior_variance::Float64, prior_sample_size::Float64, addIntercept::Bool, reml::Bool, assumption::String, method::String, optim_interval::Int64, permutation_test::Bool, nperms::Int64, rndseed::Int64, profileLL::Bool, markerID::Int64, h2_grid::Vector{Float64}, decomp_scheme::String, output_pvals::Bool, chisq_df::Int64)
    @ BulkLMM ~/.julia/packages/BulkLMM/bdDFk/src/scan.jl:215

It seems like there's an issue with the weights data type, but I'm not sure how to fix it or if this is just an issue with the program.

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