diff options
Diffstat (limited to 'src/param.h')
| -rw-r--r-- | src/param.h | 12 |
1 files changed, 8 insertions, 4 deletions
diff --git a/src/param.h b/src/param.h index d3ce686..046f543 100644 --- a/src/param.h +++ b/src/param.h @@ -160,6 +160,8 @@ public: string file_ksnps; // File SNPs for computing K string file_gwasnps; // File SNPs for computing GWAS + bool is_mdb; + // QC-related parameters. double miss_level; double maf_level; @@ -336,17 +338,16 @@ public: void CheckParam(); void CheckData(); void PrintSummary(); - void ReadGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K); - void ReadGenotypes(vector<vector<unsigned char>> &Xt, gsl_matrix *K, - const bool calc_K); + void ReadBIMBAMGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K); void CheckCvt(); void CopyCvt(gsl_matrix *W); void CopyA(size_t flag, gsl_matrix *A); void CopyGxe(gsl_vector *gxe); void CopyWeight(gsl_vector *w); - void ProcessCvtPhen(); + void ProcessInclusionIndicators(); void CopyCvtPhen(gsl_matrix *W, gsl_vector *y, size_t flag); void CopyCvtPhen(gsl_matrix *W, gsl_matrix *Y, size_t flag); + gsl_matrix *MdbCalcKin(); void CalcKin(gsl_matrix *matrix_kin); void CalcS(const map<string, double> &mapRS2wA, const map<string, double> &mapRS2wK, const gsl_matrix *W, @@ -368,6 +369,9 @@ public: const map<string, double> &mapRS2z, gsl_vector *w, gsl_vector *z, vector<size_t> &vec_cat); void UpdateSNP(const map<string, double> &mapRS2wA); + + inline bool is_loco() { return !loco.empty(); } + }; size_t GetabIndex(const size_t a, const size_t b, const size_t n_cvt); |