diff options
Diffstat (limited to 'test/dev_tests.rb')
| -rw-r--r-- | test/dev_tests.rb | 34 |
1 files changed, 27 insertions, 7 deletions
diff --git a/test/dev_tests.rb b/test/dev_tests.rb index fb3fecf..fc2f7bb 100644 --- a/test/dev_tests.rb +++ b/test/dev_tests.rb @@ -10,7 +10,7 @@ class TestQuick < MiniTest::Test end def test_linear_model - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + gemma("-g ./example/mouse_hs1940.geno.txt.gz \ -p ./example/mouse_hs1940.pheno.txt \ -n 1 \ -a ./example/mouse_hs1940.anno.txt \ @@ -23,14 +23,14 @@ class TestQuick < MiniTest::Test end def test_BXD - assert gemma("-g ./example/BXD_geno.txt.gz \ + 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") - assert gemma("-g ./example/BXD_geno.txt.gz \ + gemma("-g ./example/BXD_geno.txt.gz \ -p ./example/BXD_pheno.txt \ -c ./example/BXD_covariates2.txt \ -a ./example/BXD_snps.txt \ @@ -39,18 +39,18 @@ class TestQuick < MiniTest::Test -o BXDLMM") expect("output/BXDLMM.assoc.txt",[[2,9,"1.234747e-01"], - [:max,9,"9.997119e-01"]]) + [:max,"p_lrt","9.997119e-01"]]) end def test_mouse_hs1940_loco - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + 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") - assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \ + gemma("-g ./example/mouse_hs1940.geno.txt.gz \ -p ./example/mouse_hs1940.pheno.txt \ -n 1 \ -loco 1 \ @@ -61,6 +61,26 @@ class TestQuick < MiniTest::Test -nind 400 -no-check \ -o mouse_hs1940_loco") expect("output/mouse_hs1940_loco.assoc.txt",[[2,9,"-3.073643e+02"], - [:max,11,"9.716047e-01"]]) + [: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 |