├── .gitignore ├── README.md ├── include ├── .macros.h.swo ├── ExternalInterface.h ├── InputMatrix.h ├── InputMatrixBedInCore.h ├── InputMatrixCSV.h ├── InputMatrixEigenInCore.h ├── InputMatrixEigenstrat.h ├── InputMatrixGeneralBinary.h ├── InputMatrixMemory.h ├── ezOptionParser.hpp ├── fastpca_diffsnorm.hpp ├── fastpca_io.hpp ├── fastpca_linear_algebra.hpp ├── fastpca_pca.hpp └── macros.h ├── lib ├── generate_custom_mkl.sh ├── libfastpca_custommkl.dylib ├── libfastpca_custommkl.so ├── libiomp5.dylib ├── libiomp5.so └── mkl_fxn_list ├── oocRPCA ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R │ └── oocRPCAWrappers.R ├── inst │ ├── build │ │ ├── csv2binary.linux │ │ ├── csv2binary.osx │ │ ├── fastpca.linux │ │ └── fastpca.osx │ ├── lib │ │ ├── generate_custom_mkl.sh │ │ ├── libfastpca_custommkl.dylib │ │ ├── libfastpca_custommkl.so │ │ ├── libiomp5.dylib │ │ ├── libiomp5.so │ │ └── mkl_fxn_list │ └── tests │ │ ├── example.bed │ │ ├── example.bim │ │ ├── example.fam │ │ ├── example_with_impute.bed │ │ ├── example_with_impute.bim │ │ ├── example_with_impute.fam │ │ ├── testthat.R │ │ └── testthat │ │ ├── testSmallMatrices.R │ │ └── test_csv.csv ├── man │ ├── oocPCA_BIN.Rd │ ├── oocPCA_CSV.Rd │ ├── oocPCA_base.Rd │ └── oocPCA_csv2binary.Rd └── oocRPCA.Rproj ├── src ├── ExternalInterface.cpp ├── InputMatrix.cpp ├── InputMatrixBedInCore.cpp ├── InputMatrixCSV.cpp ├── InputMatrixEigenInCore.cpp ├── InputMatrixEigenstrat.cpp ├── InputMatrixGeneralBinary.cpp ├── InputMatrixMemory.cpp ├── Makefile ├── csv2binary │ └── csv2binary.cpp ├── fastpca_diffsnorm.cpp ├── fastpca_io.cpp ├── fastpca_linear_algebra.cpp ├── fastpca_pca.cpp └── main.cpp └── testing ├── TestingSuite.m └── example_with_impute.eigenstratgeno /.gitignore: -------------------------------------------------------------------------------- 1 | *.swp 2 | *.o 3 | -------------------------------------------------------------------------------- /README.md: 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