diff options
Diffstat (limited to 'src/io.h')
| -rw-r--r-- | src/io.h | 72 |
1 files changed, 55 insertions, 17 deletions
@@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + Copyright (C) 2011-2017, Xiang Zhou This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -121,22 +121,60 @@ bool ReadFile_gene (const string &file_gene, vector<double> &vec_read, vector<SNPINFO> &snpInfo, size_t &ng_total); bool ReadHeader_io (const string &line, HEADER &header); -bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, size_t &n_vc); -bool ReadFile_mcat (const string &file_mcat, map<string, size_t> &mapRS2cat, size_t &n_vc); - -bool ReadFile_catc (const string &file_cat, map<string, vector<double> > &mapRS2catc, size_t &n_cat); -bool ReadFile_mcatc (const string &file_mcat, map<string, vector<double> > &mapRS2catc, size_t &n_cat); - -bool BimbamKin (const string &file_geno, const int display_pace, const vector<int> &indicator_idv, const vector<int> &indicator_snp, const map<string, double> &mapRS2weight, const map<string, size_t> &mapRS2cat, const vector<SNPINFO> &snpInfo, const gsl_matrix *W, gsl_matrix *matrix_kin, gsl_vector *vector_ns); -bool PlinkKin (const string &file_bed, const int display_pace, const vector<int> &indicator_idv, const vector<int> &indicator_snp, const map<string, double> &mapRS2weight, const map<string, size_t> &mapRS2cat, const vector<SNPINFO> &snpInfo, const gsl_matrix *W, gsl_matrix *matrix_kin, gsl_vector *vector_ns); -bool MFILEKin (const size_t mfile_mode, const string &file_mfile, const int display_pace, const vector<int> &indicator_idv, const vector<vector<int> > &mindicator_snp, const map<string, double> &mapRS2weight, const map<string, size_t> &mapRS2cat, const vector<vector<SNPINFO> > &msnpInfo, const gsl_matrix *W, gsl_matrix *matrix_kin, gsl_vector *vector_ns); - -bool ReadFile_wsnp (const string &file_wsnp, map<string, double> &mapRS2double); -bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc, map<string, vector<double> > &mapRS2vector); - -void ReadFile_beta (const string &file_beta, const map<string, size_t> &mapRS2cat, const map<string, double> &mapRS2wA, vector<size_t> &vec_cat, vector<size_t> &vec_ni, vector<double> &vec_weight, vector<double> &vec_z2, size_t &ni_total, size_t &ns_total, size_t &ns_test); -void ReadFile_beta (const string &file_beta, const map<string, double> &mapRS2wA, map<string, string> &mapRS2A1, map<string, double> &mapRS2z); -void Calcq (const size_t n_block, const vector<size_t> &vec_cat, const vector<size_t> &vec_ni, const vector<double> &vec_weight, const vector<double> &vec_z2, gsl_matrix *Vq, gsl_vector *q, gsl_vector *s); +bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, + size_t &n_vc); +bool ReadFile_mcat (const string &file_mcat, map<string, size_t> &mapRS2cat, + size_t &n_vc); + +bool ReadFile_catc (const string &file_cat, + map<string, vector<double> > &mapRS2catc, + size_t &n_cat); +bool ReadFile_mcatc (const string &file_mcat, map<string, + vector<double> > &mapRS2catc, size_t &n_cat); + +bool BimbamKin (const string &file_geno, const int display_pace, + const vector<int> &indicator_idv, + const vector<int> &indicator_snp, + const map<string, double> &mapRS2weight, + const map<string, size_t> &mapRS2cat, + const vector<SNPINFO> &snpInfo, const gsl_matrix *W, + gsl_matrix *matrix_kin, gsl_vector *vector_ns); +bool PlinkKin (const string &file_bed, const int display_pace, + const vector<int> &indicator_idv, + const vector<int> &indicator_snp, + const map<string, double> &mapRS2weight, + const map<string, size_t> &mapRS2cat, + const vector<SNPINFO> &snpInfo, + const gsl_matrix *W, gsl_matrix *matrix_kin, + gsl_vector *vector_ns); +bool MFILEKin (const size_t mfile_mode, const string &file_mfile, + const int display_pace, const vector<int> &indicator_idv, + const vector<vector<int> > &mindicator_snp, + const map<string, double> &mapRS2weight, + const map<string, size_t> &mapRS2cat, + const vector<vector<SNPINFO> > &msnpInfo, + const gsl_matrix *W, gsl_matrix *matrix_kin, + gsl_vector *vector_ns); + +bool ReadFile_wsnp (const string &file_wsnp, + map<string, double> &mapRS2double); +bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc, + map<string, vector<double> > &mapRS2vector); + +void ReadFile_beta (const string &file_beta, + const map<string, size_t> &mapRS2cat, + const map<string, double> &mapRS2wA, + vector<size_t> &vec_cat, vector<size_t> &vec_ni, + vector<double> &vec_weight, vector<double> &vec_z2, + size_t &ni_total, size_t &ns_total, size_t &ns_test); +void ReadFile_beta (const string &file_beta, + const map<string, double> &mapRS2wA, + map<string, string> &mapRS2A1, + map<string, double> &mapRS2z); +void Calcq (const size_t n_block, const vector<size_t> &vec_cat, + const vector<size_t> &vec_ni, + const vector<double> &vec_weight, const vector<double> &vec_z2, + gsl_matrix *Vq, gsl_vector *q, gsl_vector *s); void ReadFile_study (const string &file_study, gsl_matrix *Vq, gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni); |