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| author | xiangzhou | 2016-08-17 15:00:35 -0400 |
|---|---|---|
| committer | xiangzhou | 2016-08-17 15:00:35 -0400 |
| commit | 03d7d2556a9284dc0ac3e155b5c9a8d69b1b21ee (patch) | |
| tree | 9bb5410dc2874aba973a738a30d5a9eb7c618711 /src | |
| parent | 96e75a1dc4a46550f25d2012fa6d0874388b3282 (diff) | |
| download | pangemma-03d7d2556a9284dc0ac3e155b5c9a8d69b1b21ee.tar.gz | |
version 0.95alpha
Diffstat (limited to 'src')
| -rw-r--r-- | src/gemma.cpp | 13 |
1 files changed, 6 insertions, 7 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 54f1d3c..682835f 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -42,7 +42,6 @@ #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" @@ -53,7 +52,6 @@ #include "lmm.h" #include "mvlmm.h" #include "prdt.h" -#include "varcov.h" #include "mathfunc.h" #endif @@ -1349,6 +1347,7 @@ 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; @@ -1364,7 +1363,7 @@ 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) { @@ -1472,7 +1471,7 @@ void GEMMA::BatchRun (PARAM &cPar) gsl_vector_free (s); } - + /* //Calculate SNP covariance if (cPar.a_mode==71) { VARCOV cVarcov; @@ -1486,7 +1485,7 @@ 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 @@ -2400,7 +2399,7 @@ void GEMMA::BatchRun (PARAM &cPar) } - + /* //LDR if (cPar.a_mode==14) { gsl_vector *y=gsl_vector_alloc (cPar.ni_test); @@ -2428,7 +2427,7 @@ 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; |