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| author | xiangzhou | 2016-05-23 17:17:22 -0400 |
|---|---|---|
| committer | xiangzhou | 2016-05-23 17:17:22 -0400 |
| commit | d222159e9629f50aed78b8ecc42faef33ee96e1a (patch) | |
| tree | ad94020a629c5627b167a623fdc62784d70e7eed | |
| parent | 943e970c9cbc184dcca679fbe455f48c32242cdc (diff) | |
| download | pangemma-d222159e9629f50aed78b8ecc42faef33ee96e1a.tar.gz | |
version 0.95alpha
| -rw-r--r-- | src/gemma.cpp | 17 |
1 files changed, 9 insertions, 8 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 3b9fe29..55eb1ee 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -43,7 +43,7 @@ #include "lmm_float.h" //for LMM class, and functions CalcLambda, CalcPve, CalcVgVe #include "mvlmm_float.h" //for MVLMM class #include "prdt_float.h" //for PRDT class -#include "varcov_float.h" //for MVLMM class + #include "mathfunc_float.h" //for a few functions #else #include "io.h" @@ -51,11 +51,11 @@ #include "vc.h" #include "lm.h" #include "bslmm.h" -#include "ldr.h" + #include "lmm.h" #include "mvlmm.h" #include "prdt.h" -#include "varcov.h" + #include "mathfunc.h" #endif @@ -1351,6 +1351,7 @@ void GEMMA::BatchRun (PARAM &cPar) gsl_matrix_free (G); } + /* //Compute the LDSC weights (not implemented yet) if (cPar.a_mode==72) { cout<<"Calculating Weights ... "<<endl; @@ -1366,7 +1367,7 @@ void GEMMA::BatchRun (PARAM &cPar) cVarcov.CopyToParam(cPar); } - + */ //Compute the S matrix (and its variance), that is used for variance component estimation using summary statistics if (cPar.a_mode==25 || cPar.a_mode==26) { @@ -1474,7 +1475,7 @@ void GEMMA::BatchRun (PARAM &cPar) gsl_vector_free (s); } - + /* //Calculate SNP covariance if (cPar.a_mode==71) { VARCOV cVarcov; @@ -1488,7 +1489,7 @@ void GEMMA::BatchRun (PARAM &cPar) cVarcov.CopyToParam(cPar); } - + */ //LM if (cPar.a_mode==51 || cPar.a_mode==52 || cPar.a_mode==53 || cPar.a_mode==54) { //Fit LM @@ -2402,7 +2403,7 @@ void GEMMA::BatchRun (PARAM &cPar) } - + /* //LDR if (cPar.a_mode==14) { gsl_vector *y=gsl_vector_alloc (cPar.ni_test); @@ -2430,7 +2431,7 @@ void GEMMA::BatchRun (PARAM &cPar) gsl_matrix_free (W); gsl_matrix_free (G); } - + */ cPar.time_total=(clock()-time_begin)/(double(CLOCKS_PER_SEC)*60.0); return; |