| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | lm.cpp | 130 << sumStat[t].se << "\t" << sumStat[t].p_wald << endl; in WriteFiles()
139 << sumStat[t].se << "\t" << sumStat[t].p_wald << "\t" in WriteFiles()
203 << sumStat[t].se << "\t" << sumStat[t].p_wald << endl; in WriteFiles()
211 << sumStat[t].se << "\t" << sumStat[t].p_wald << "\t" in WriteFiles()
268 double &beta, double &se, double &p_wald, double &p_lrt, in LmCalcP() argument
277 p_wald = gsl_cdf_fdist_Q(beta * beta / (se_wald * se_wald), 1.0, df); in LmCalcP()
303 double beta = 0, se = 0, p_wald = 0, p_lrt = 0, p_score = 0; in AnalyzeGene() local
363 SUMSTAT SNPs = {beta, se, 0.0, 0.0, p_wald, p_lrt, p_score, -0.0 }; in AnalyzeGene()
395 double beta = 0, se = 0, p_wald = 0, p_lrt = 0, p_score = 0; in AnalyzeBimbam() local
477 SUMSTAT SNPs = {beta, se, 0.0, 0.0, p_wald, p_lrt, p_score, -0.0}; in AnalyzeBimbam()
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| H A D | lmm.cpp | 156 << st.p_wald << endl; in WriteFiles()
168 << st.p_wald << "\t" in WriteFiles()
1118 double &se, double &p_wald) { in CalcRLWald() argument
1151 p_wald = gsl_cdf_fdist_Q((P_yy - Px_yy) * tau, 1.0, df); in CalcRLWald()
1436 CalcRLWald(lambda_remle, param1, beta, se, p_wald); in AnalyzeGene()
1536 CalcRLWald(lambda_remle, param1, beta, se, p_wald); in Analyze()
1548 p_wald, p_lrt, p_score, logl_H1}; in Analyze()
1858 CalcRLWald(lambda_remle, param1, beta, se, p_wald); in AnalyzePlink()
1870 p_wald, p_lrt, p_score, logl_H1}; in AnalyzePlink()
2343 CalcRLWald(lambda_remle, param1, beta, se, p_wald); in AnalyzeBimbamGXE()
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| H A D | param.h | 60 double p_wald; // p value from a Wald test. variable
72 double p_wald; // p value from a Wald test. variable
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| H A D | mvlmm.cpp | 193 outfile << sumStat[t].p_wald << endl; in WriteFiles()
199 outfile << sumStat[t].p_wald << "\t" << sumStat[t].p_lrt << "\t" in WriteFiles()
2987 double logl_H0 = 0.0, logl_H1 = 0.0, p_wald = 0, p_lrt = 0, p_score = 0; in AnalyzeBimbam() local
3333 if (p_wald < p_nr) { in AnalyzeBimbam()
3341 p_wald = PCRT(1, d_size, p_wald, crt_a, crt_b, crt_c); in AnalyzeBimbam()
3809 if (p_wald < p_nr) { in AnalyzePlink()
3817 p_wald = PCRT(1, d_size, p_wald, crt_a, crt_b, crt_c); in AnalyzePlink()
4325 if (p_wald < p_nr) { in AnalyzeBimbamGXE()
4333 p_wald = PCRT(1, d_size, p_wald, crt_a, crt_b, crt_c); in AnalyzeBimbamGXE()
4801 if (p_wald < p_nr) { in AnalyzePlinkGXE()
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| H A D | lmm.h | 122 double &se, double &p_wald);
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| /dports/biology/gemma/GEMMA-0.98.3/doc/ |
| H A D | manual.tex | 803 chr rs ps n_mis n_obs allele1 allele0 af beta se p_wald
1012 chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald
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