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| author | Pjotr Prins | 2025-11-27 10:45:42 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2025-11-27 10:45:42 +0100 |
| commit | 6abb0ce062f27e15a4168fca80939bc7600d781d (patch) | |
| tree | 8361dd17aa97310907714440f3d2c6470dbdc876 /src/gemma.cpp | |
| parent | 6bd0ea3e2a245c3f86f66505eec118296ae04d30 (diff) | |
| download | pangemma-6abb0ce062f27e15a4168fca80939bc7600d781d.tar.gz | |
Changing namings to bimbam to make clearer
Diffstat (limited to 'src/gemma.cpp')
| -rw-r--r-- | src/gemma.cpp | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 01e80f7..38b4913 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -2901,7 +2901,7 @@ void GEMMA::BatchRun(PARAM &cPar) { // run bvsr if rho==1 if (cPar.rho_min == 1 && cPar.rho_max == 1) { // read genotypes X (not UtX) - cPar.ReadGenotypes(UtX, G, false); + cPar.ReadBIMBAMGenotypes(UtX, G, false); // perform BSLMM analysis BSLMM cBslmm; @@ -2919,7 +2919,7 @@ void GEMMA::BatchRun(PARAM &cPar) { // read relatedness matrix G if (!(cPar.file_kin).empty()) { - cPar.ReadGenotypes(UtX, G, false); + cPar.ReadBIMBAMGenotypes(UtX, G, false); // read relatedness matrix G ReadFile_kin(cPar.file_kin, cPar.indicator_idv, cPar.mapID2num, @@ -2933,7 +2933,7 @@ void GEMMA::BatchRun(PARAM &cPar) { CenterMatrix(G); validate_K(G); } else { - cPar.ReadGenotypes(UtX, G, true); + cPar.ReadBIMBAMGenotypes(UtX, G, true); } // eigen-decomposition and calculate trace_G @@ -3011,7 +3011,7 @@ void GEMMA::BatchRun(PARAM &cPar) { // run bvsr if rho==1 if (cPar.rho_min == 1 && cPar.rho_max == 1) { // read genotypes X (not UtX) - cPar.ReadGenotypes(UtX, G, false); + cPar.ReadBIMBAMGenotypes(UtX, G, false); // perform BSLMM analysis BSLMM cBslmm; @@ -3030,7 +3030,7 @@ void GEMMA::BatchRun(PARAM &cPar) { // read relatedness matrix G if (!(cPar.file_kin).empty()) { - cPar.ReadGenotypes(UtX, G, false); + cPar.ReadBIMBAMGenotypes(UtX, G, false); // read relatedness matrix G ReadFile_kin(cPar.file_kin, cPar.indicator_idv, cPar.mapID2num, @@ -3045,7 +3045,7 @@ void GEMMA::BatchRun(PARAM &cPar) { validate_K(G); } else { - cPar.ReadGenotypes(UtX, G, true); + cPar.ReadBIMBAMGenotypes(UtX, G, true); } // eigen-decomposition and calculate trace_G |