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require 'minitest/autorun'
require 'lib/test-helpers'
class TestQuick < MiniTest::Test
include TestHelpers
def setup
ENV['GSL_RNG_SEED']=100.to_s
end
def test_linear_model
gemma("-g ./example/mouse_hs1940.geno.txt.gz \
-p ./example/mouse_hs1940.pheno.txt \
-n 1 \
-a ./example/mouse_hs1940.anno.txt \
-lm \
-o mouse_hs1940_CD8_lm")
expect('output/mouse_hs1940_CD8_lm.assoc.txt',[[2,1,"rs3707673"],
[2,10,"5.252187e-05"],
[3,9,"3.909916e-02"]])
end
def test_BXD
gemma("-g ./example/BXD_geno.txt.gz \
-p ./example/BXD_pheno.txt \
-c ./example/BXD_covariates2.txt \
-a ./example/BXD_snps.txt \
-gk \
-o BXD")
gemma("-g ./example/BXD_geno.txt.gz \
-p ./example/BXD_pheno.txt \
-c ./example/BXD_covariates2.txt \
-a ./example/BXD_snps.txt \
-k ./output/BXD.cXX.txt \
-lmm 2 -no-check -maf 0.1 \
-o BXDLMM")
expect("output/BXDLMM.assoc.txt",[[2,9,"1.234747e-01"],
[:max,"p_lrt","9.997119e-01"]])
gemma("-g ./example/BXD_geno.txt.gz \
-p ./example/BXD_pheno.txt \
-c ./example/BXD_covariates2.txt \
-a ./example/BXD_snps.txt \
-k ./output/BXD.cXX.txt \
-lmm 9 -no-check -maf 0.1 \
-o BXDLMM9")
expect("output/BXDLMM9.assoc.txt",[[:max,"l_mle","0.7531109"],
[:max,"p_lrt","9.997119e-01"]])
end
def test_mouse_hs1940_loco
gemma("-g ./example/mouse_hs1940.geno.txt.gz \
-p ./example/mouse_hs1940.pheno.txt \
-a ./example/mouse_hs1940.anno.txt \
-snps ./example/mouse_hs1940_snps.txt \
-nind 400 -loco 1 -gk \
-o mouse_hs1940_loco")
gemma("-g ./example/mouse_hs1940.geno.txt.gz \
-p ./example/mouse_hs1940.pheno.txt \
-n 1 \
-loco 1 \
-a ./example/mouse_hs1940.anno.txt \
-k ./output/mouse_hs1940_loco.cXX.txt \
-snps ./example/mouse_hs1940_snps.txt \
-lmm \
-nind 400 -no-check \
-o mouse_hs1940_loco")
expect("output/mouse_hs1940_loco.assoc.txt",[[2,9,"-3.073643e+02"],
[:max,"p_wald","9.716047e-01"]])
end
# Test for https://github.com/genetics-statistics/GEMMA/issues/58
# fixed GSLv2 NaN's that appeared with covariates.
def test_plink_covariates_lmm
gemma("-bfile example/HLC -gk 2 -o testPlinkStandardRelatednessMatrixK")
gemma("-bfile example/HLC \
-k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
-lmm 1 \
-maf 0.1 \
-c example/HLC_covariates.txt \
-no-check \
-o plink_lmm1_cov")
expect("output/plink_lmm1_cov.assoc.txt",[[100,"p_wald","5.189953e-01"],
[:max,"logl_H1","279.2689"],
[:max,"l_remle","1.686062"],
[:max,"p_wald","0.9999996"]])
end
end
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