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| author | xiangzhou | 2016-07-24 15:58:31 -0400 |
|---|---|---|
| committer | xiangzhou | 2016-07-24 15:58:31 -0400 |
| commit | 60f86db94ee2b4f826300cb0e73cb658ac7bdfd8 (patch) | |
| tree | 4f3eeb1b0575493b8f29262a2acdc8f6a432633c /src/gemma.cpp | |
| parent | d222159e9629f50aed78b8ecc42faef33ee96e1a (diff) | |
| download | pangemma-60f86db94ee2b4f826300cb0e73cb658ac7bdfd8.tar.gz | |
version 0.95alpha
Diffstat (limited to 'src/gemma.cpp')
| -rw-r--r-- | src/gemma.cpp | 19 |
1 files changed, 9 insertions, 10 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 55eb1ee..c85670d 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 @@ -65,7 +65,7 @@ using namespace std; GEMMA::GEMMA(void): -version("0.95alpha"), date("07/11/2015"), year("2011") +version("0.95alpha"), date("07/24/2016"), year("2011") {} void GEMMA::PrintHeader (void) @@ -1351,7 +1351,6 @@ 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; @@ -1367,7 +1366,7 @@ 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) { @@ -1475,7 +1474,7 @@ void GEMMA::BatchRun (PARAM &cPar) gsl_vector_free (s); } - /* + //Calculate SNP covariance if (cPar.a_mode==71) { VARCOV cVarcov; @@ -1489,7 +1488,7 @@ 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 @@ -2403,7 +2402,7 @@ void GEMMA::BatchRun (PARAM &cPar) } - /* + //LDR if (cPar.a_mode==14) { gsl_vector *y=gsl_vector_alloc (cPar.ni_test); @@ -2431,7 +2430,7 @@ 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; |