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joshua-slaughterjoshua-slaughter
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Adding unwatched files for testing GWEIS
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‎test/data/config_gweis_first_order.yaml‎

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type: gweis
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extra_treatments:
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- 22001
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outcome_extra_covariates:
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- COV_1
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extra_confounders:
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- 21003

‎test/data/config_gweis_higher_order.yaml‎

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type: gweis
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extra_treatments:
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- 22001
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- BINARY_1
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- BINARY_2
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outcome_extra_covariates:
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- COV_1
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extra_confounders:
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- 21003

‎test/inputs_from_gweis_config.jl‎

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module TestGweisEstimands
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using Test
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using SnpArrays
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using TargeneCore
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using Arrow
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using DataFrames
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using Serialization
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using TMLE
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using CSV
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TESTDIR = joinpath(pkgdir(TargeneCore), "test")
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include(joinpath(TESTDIR, "testutils.jl"))
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function get_summary_stats(estimands)
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outcomes = [TargeneCore.get_outcome(Ψ) for Ψ in estimands]
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results = DataFrame(ESTIMAND = estimands, OUTCOME = outcomes)
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return sort(combine(groupby(results, :OUTCOME), nrow), :OUTCOME)
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end
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function check_estimands_levels_interactions(estimands)
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for Ψ in estimands
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# If the two components are present, the first is the 0 -> 1 and the second is the 1 -> 2
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# The variant should always be the last key
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variant = last(collect(keys(Ψ.args[1].treatment_values)))
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if length(Ψ.args) == 2
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@test Ψ.args[1].treatment_values[variant] == (control = 0x00, case = 0x01)
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@test Ψ.args[2].treatment_values[variant] == (control = 0x01, case = 0x02)
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else
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# Otherwise we check they are one or the other
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arg = only(Ψ.args)
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@test arg.treatment_values[variant]==(control = 0x00, case = 0x01) ||
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arg.treatment_values[variant]==( control = 0x01, case = 0x02)
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end
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end
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end
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@testset "Test inputs_from_config gweis: no positivity constraint" begin
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tmpdir = mktempdir()
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copy!(ARGS, [
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"estimation-inputs",
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joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"),
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string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")),
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string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")),
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string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")),
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string("--outprefix=", joinpath(tmpdir, "final")),
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"--batchsize=5",
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"--verbosity=0",
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"--positivity-constraint=0"
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])
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TargeneCore.julia_main()
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# Check dataset
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dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow")))
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@test size(dataset) == (1940, 886)
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# Check estimands
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estimands = []
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for file in readdir(tmpdir, join=true)
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if endswith(file, "jls")
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append!(estimands, deserialize(file).estimands)
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end
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end
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@test all(e isa JointEstimand for e in estimands)
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# There are 875 variants in the dataset
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summary_stats = get_summary_stats(estimands)
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@test summary_stats == DataFrame(
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OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1],
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nrow = repeat([875], 5)
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)
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check_estimands_levels_interactions(estimands)
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end
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@testset "Test inputs_from_config gweis: positivity constraint" begin
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tmpdir = mktempdir()
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copy!(ARGS, [
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"estimation-inputs",
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joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"),
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string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")),
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string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")),
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string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")),
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string("--outprefix=", joinpath(tmpdir, "final")),
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"--batchsize=5",
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"--verbosity=0",
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"--positivity-constraint=0.2"
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])
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TargeneCore.julia_main()
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# Check dataset
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dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow")))
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@test size(dataset) == (1940, 886)
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# Check estimands
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estimands = []
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for file in readdir(tmpdir, join=true)
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if endswith(file, "jls")
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append!(estimands, deserialize(file).estimands)
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end
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end
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# The positivity constraint reduces the number of variants
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@test all(e isa JointEstimand for e in estimands)
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summary_stats = get_summary_stats(estimands)
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@test summary_stats == DataFrame(
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OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1],
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nrow = repeat([142], 5)
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)
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check_estimands_levels_interactions(estimands)
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end
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@testset "Test inputs_from_config gweis: no positivity constraint and four-point interaction" begin
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tmpdir = mktempdir()
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copy!(ARGS, [
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"estimation-inputs",
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joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"),
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string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")),
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string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")),
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string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")),
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string("--outprefix=", joinpath(tmpdir, "final")),
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"--batchsize=5",
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"--verbosity=0",
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"--positivity-constraint=0"
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])
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TargeneCore.julia_main()
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# Check dataset
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dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow")))
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@test size(dataset) == (1940, 886)
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# Check estimands
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estimands = []
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for file in readdir(tmpdir, join=true)
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if endswith(file, "jls")
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append!(estimands, deserialize(file).estimands)
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end
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end
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@test all(e isa JointEstimand for e in estimands)
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# There are 875 variants in the dataset
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summary_stats = get_summary_stats(estimands)
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@test summary_stats == DataFrame(
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OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1],
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nrow = repeat([875], 3)
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)
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check_estimands_levels_interactions(estimands)
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end
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@testset "Test inputs_from_config gweis: positivity constraint and four-point interaction" begin
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tmpdir = mktempdir()
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copy!(ARGS, [
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"estimation-inputs",
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joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"),
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string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")),
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string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")),
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string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")),
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string("--outprefix=", joinpath(tmpdir, "final")),
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"--batchsize=5",
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"--verbosity=0",
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"--positivity-constraint=0.02"
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])
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TargeneCore.julia_main()
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# Check dataset
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dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow")))
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@test size(dataset) == (1940, 886)
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# Check estimands
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estimands = []
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for file in readdir(tmpdir, join=true)
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if endswith(file, "jls")
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append!(estimands, deserialize(file).estimands)
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end
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end
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@test all(e isa JointEstimand for e in estimands)
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# There are 784 treatments in the dataset after positivity_constraint
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summary_stats = get_summary_stats(estimands)
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@test summary_stats == DataFrame(
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OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1],
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nrow = repeat([784], 3)
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)
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check_estimands_levels_interactions(estimands)
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end
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end
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true

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