diff options
| -rw-r--r-- | src/lmm.cpp | 20 | ||||
| -rw-r--r-- | test/dev_tests.rb | 11 |
2 files changed, 21 insertions, 10 deletions
diff --git a/src/lmm.cpp b/src/lmm.cpp index 3a57d76..1366553 100644 --- a/src/lmm.cpp +++ b/src/lmm.cpp @@ -1425,7 +1425,7 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval, CalcUab(UtW, Uty, Uab); FUNC_PARAM param0 = {false, ni_test, n_cvt, eval, Uab, ab, 0}; - if (a_mode == M_LMM2 || a_mode == M_LMM3 || a_mode == M_LMM4) { + if (a_mode == M_LMM2 || a_mode == M_LMM3 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcLambda('L', param0, l_min, l_max, n_region, l_H0, logl_H0); } @@ -1434,7 +1434,7 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval, FUNC_PARAM param1 = {false, ni_test, n_cvt, eval, Uab, ab, 0}; // 3 is before 1. - if (a_mode == M_LMM3 || a_mode == M_LMM4) { + if (a_mode == M_LMM3 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcRLScore(l_H0, param1, beta, se, p_score); } @@ -1443,7 +1443,7 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval, CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == M_LMM2 || a_mode == M_LMM4) { + if (a_mode == M_LMM2 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_H0), 1); } @@ -1543,7 +1543,7 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp, CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == M_LMM2 || a_mode == M_LMM9 || a_mode == M_LMM4) { + if (a_mode == M_LMM2 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_mle_H0), 1); } @@ -1855,7 +1855,7 @@ void LMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, FUNC_PARAM param1 = {false, ni_test, n_cvt, eval, Uab, ab, 0}; // 3 is before 1, for beta. - if (a_mode == M_LMM3 || a_mode == M_LMM4) { + if (a_mode == M_LMM3 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcRLScore(l_mle_null, param1, beta, se, p_score); } @@ -1866,7 +1866,7 @@ void LMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval, CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == M_LMM2 || a_mode == M_LMM4) { + if (a_mode == M_LMM2 || a_mode == M_LMM4 || a_mode == M_LMM9) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_mle_H0), 1); } @@ -2382,7 +2382,7 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval, FUNC_PARAM param1 = {false, ni_test, n_cvt + 2, eval, Uab, ab, 0}; // 3 is before 1. - if (a_mode == 3 || a_mode == 4) { + if (a_mode == 3 || a_mode == 4 || a_mode == 9) { CalcRLScore(l_mle_null, param1, beta, se, p_score); } @@ -2391,7 +2391,7 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval, CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == 2 || a_mode == 4) { + if (a_mode == 2 || a_mode == 4 || a_mode == 9) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_H0), 1); } @@ -2560,7 +2560,7 @@ void LMM::AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval, FUNC_PARAM param1 = {false, ni_test, n_cvt + 2, eval, Uab, ab, 0}; // 3 is before 1, for beta. - if (a_mode == 3 || a_mode == 4) { + if (a_mode == 3 || a_mode == 4 || a_mode == 9) { CalcRLScore(l_mle_null, param1, beta, se, p_score); } @@ -2569,7 +2569,7 @@ void LMM::AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval, CalcRLWald(lambda_remle, param1, beta, se, p_wald); } - if (a_mode == 2 || a_mode == 4) { + if (a_mode == 2 || a_mode == 4 || a_mode == 9) { CalcLambda('L', param1, l_min, l_max, n_region, lambda_mle, logl_H1); p_lrt = gsl_cdf_chisq_Q(2.0 * (logl_H1 - logl_H0), 1); } diff --git a/test/dev_tests.rb b/test/dev_tests.rb index fc2f7bb..49068dc 100644 --- a/test/dev_tests.rb +++ b/test/dev_tests.rb @@ -40,6 +40,17 @@ class TestQuick < MiniTest::Test 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 |