[Genabel-commits] r1172 - pkg/ProbABEL/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 24 01:22:30 CET 2013
Author: maartenk
Date: 2013-03-24 01:22:30 +0100 (Sun, 24 Mar 2013)
New Revision: 1172
Modified:
pkg/ProbABEL/src/main.cpp
Log:
removed commented code and removed not needed variable from function
Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp 2013-03-23 15:38:09 UTC (rev 1171)
+++ pkg/ProbABEL/src/main.cpp 2013-03-24 00:22:30 UTC (rev 1172)
@@ -330,9 +330,10 @@
}
}
-int get_start_position(const cmdvars& input_var, int model, int start_pos,
+int get_start_position(const cmdvars& input_var, int model,
int number_of_rows_or_columns)
{
+ int start_pos;
if (!input_var.getAllcov() && model == 0 && input_var.getInteraction() == 0)
{
if (input_var.getNgpreds() == 2)
@@ -374,47 +375,17 @@
input_var.set_variables(argc, argv);
input_var.printinfo();
- // if (allcov && ngpreds>1)
- // {
- // cout << "\n\n"
- // << "WARNING: --allcov allowed only for 1 predictor (MLDOSE)\n";
- // allcov = 0;
- // }
+
mlinfo mli(input_var.getMlinfofilename(), input_var.getMapfilename());
int nsnps = mli.nsnps;
phedata phd;
int interaction_cox = create_phenotype(phd, input_var);
- //interaction--;
- // if (input_var.getInverseFilename()!= NULL && phd.ncov > 1)
- // {
- // std::cerr << "Error: In mmscore you can not use any covariates."
- // << " You phenotype file must conatin id column and "
- // << "trait (residuals) only\n";
- // exit(1);
- // }
- // if (input_var.getInverseFilename()!= NULL &&
- // (allcov == 1 || score == 1
- // || input_var.getInteraction()!= 0
- // || ngpreds==2))
- // {
- // std::cerr << "Error: In mmscore you can use additive model "
- // << "without any inetractions only\n";
- // exit(1);
- // }
+
masked_matrix invvarmatrix;
- /*
- * now should be possible... delete this part later when everything works
- #if LOGISTIC
- if (input_var.getInverseFilename()!= NULL)
- {
- std::cerr << "ERROR: mmscore is forbidden for logistic regression\n";
- exit(1);
- }
- #endif
- */
+
std::cout << "Reading data ..." << std::flush;
if (input_var.getInverseFilename() != NULL)
{
@@ -435,16 +406,8 @@
phd.idnames);
std::cout << " loaded genotypic data ..." << std::flush;
- /**
- if (input_var.getIsFvf())
- gendata gtd(str_genfilename, nsnps, input_var.getNgpreds(),
- phd.nids_all, phd.allmeasured, phd.idnames);
- else
- gendata gtd(input_var.getGenfilename(), nsnps,
- input_var.getNgpreds(), phd.nids_all, phd.nids,
- phd.allmeasured, skipd, phd.idnames);
- **/
+
// estimate null model
#if COXPH
coxph_data nrgd = coxph_data(phd, gtd, -1);
@@ -515,54 +478,7 @@
}
}
- //________________________________________________________________
- /*
- if (input_var.getAllcov())
- {
- if (score)
- {
- outfile << input_var.getSep() << "beta_mu"; // << input_var.getSep() << "beta_SNP_A1";
- outfile << input_var.getSep() << "sebeta_mu"; // << input_var.getSep() << "sebeta_SNP_A1";
- }
- else
- {
- for (int i =0; i<phd.n_model_terms-1;i++)
- outfile << input_var.getSep() << "beta_" << phd.model_terms[i] << input_var.getSep() << "sebeta_" << phd.model_terms[i];
- }
- if(interactio != 0) outfile << input_var.getSep() << "beta_SNP_" << phd.model_terms[interaction];
- }
- if (input_var.getNgpreds()==2)
- {
- outfile << input_var.getSep() << "beta_SNP_A1A2"
- << input_var.getSep() << "beta_SNP_A1A1"
- << input_var.getSep() << "sebeta_SNP_A1A2"
- << input_var.getSep() << "sebeta_SNP_a1A1"
- << input_var.getSep() << "chi2_SNP_2df"
- << input_var.getSep() << "beta_SNP_addA1"
- << input_var.getSep() << "sebeta_SNP_addA1"
- << input_var.getSep() << "chi2_SNP_addA1"
- << input_var.getSep() << "beta_SNP_domA1"
- << input_var.getSep() << "sebeta_SNP_domA1"
- << input_var.getSep() << "chi2_SNP_domA1"
- << input_var.getSep() << "beta_SNP_recA1"
- << input_var.getSep() << "sebeta_SNP_recA1"
- << input_var.getSep() << "chi2_SNP_recA1"
- << input_var.getSep() << "beta_SNP_odom"
- << input_var.getSep() << "sebeta_SNP_odom"
- << input_var.getSep() << "chi2_SNP_odom\n";
- }
- else
- {
- outfile << input_var.getSep() << "beta_SNP_add"
- << input_var.getSep() << "sebeta_SNP_add"
- << input_var.getSep() << "chi2_SNP_add\n";
- }
-
- */
- // exit(1);
- //________________________________________________________________
- //Maksim, 9 Jan, 2009
int maxmod = 5;
int start_pos, end_pos;
@@ -679,7 +595,7 @@
#endif
int number_of_rows_or_columns = rd.beta.nrow;
- start_pos = get_start_position(input_var, model, start_pos,
+ start_pos = get_start_position(input_var, model,
number_of_rows_or_columns);
cout << "start_pos" << start_pos << "\n";
for (int pos = start_pos; pos < rd.beta.nrow; pos++)
@@ -748,7 +664,7 @@
} else //beta, sebeta = nan
{
int number_of_rows_or_columns = rgd.X.ncol;
- start_pos = get_start_position(input_var, model, start_pos,
+ start_pos = get_start_position(input_var, model,
number_of_rows_or_columns);
if (input_var.getInteraction() != 0 && !input_var.getAllcov()
@@ -890,237 +806,8 @@
//} // end ngpreds ==1
}
+
//
-//End of All models output.
-//
-// else //Only additive model. Only one output file
-// {
-// //Write mlinfo to output:
-// int file = 0;
-// write_mlinfo(outfile, file, mli, csnp, input_var, gcount, freq);
-// int model = 0;
-// if (poly) //allel freq is not to rare
-// {
-//#if LOGISTIC
-// logistic_reg rd(rgd);
-// if (input_var.getScore())
-// rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
-// input_var.getInteraction(),
-// input_var.getNgpreds(),
-// invvarmatrix);
-// else
-// rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
-// input_var.getInteraction(),
-// input_var.getNgpreds(),
-// invvarmatrix,
-// input_var.getRobust());
-//#elif LINEAR
-// //cout << (rgd.get_unmasked_data()).nids << " 1\n";
-//#if DEBUG
-// rgd.X.print();
-// rgd.Y.print();
-//#endif
-// linear_reg rd(rgd);
-//#if DEBUG
-// rgd.X.print();
-// rgd.Y.print();
-//#endif
-// //cout << (rgd.get_unmasked_data()).nids << " 2\n";
-// if (input_var.getScore())
-// {
-//#if DEBUG
-// cout << "input_var.getScore/n";
-// nrd.residuals.print();
-// cout << CHOLTOL << " <-CHOLTOL\n";
-// cout << model << " <-model\n";
-// cout << input_var.getInteraction()
-// << " <-input_var.getInteraction()\n";
-// cout << input_var.getNgpreds()
-// << " <-input_var.getNgpreds()\n";
-// invvarmatrix.print();
-//#endif
-// rd.score(nrd.residuals, rgd, 0, CHOLTOL, model,
-// input_var.getInteraction(), input_var.getNgpreds(),
-// invvarmatrix);
-//#if DEBUG
-// rd.beta.print();
-// cout << rd.chi2_score << " <-chi2_scoren\n";
-// rd.covariance.print();
-// rd.residuals.print();
-// rd.sebeta.print();
-// cout << rd.loglik << " <-logliken\n";
-// cout << rd.sigma2 << " <-sigma2\n";
-//#endif
-// } else
-// {
-// // if(input_var.getInverseFilename()== NULL)
-// // {
-// // cout << (rgd.get_unmasked_data()).nids << " 3\n";
-//#if DEBUG
-// cout << "rd.estimate\n";
-// cout << CHOLTOL << " <-CHOLTOL\n";
-// cout << model << " <-model\n";
-// cout << input_var.getInteraction()
-// << " <-input_var.getInteraction()\n";
-// cout << input_var.getNgpreds()
-// << " <-input_var.getNgpreds()\n";
-// cout << input_var.getRobust()
-// << " <-input_var.getRobust()\n";
-// cout << "start invarmatrix\n";
-// invvarmatrix.print();
-// cout << "end invarmatrix\n";
-// cout << rgd.is_interaction_excluded
-// << " <-rgd.is_interaction_excluded\n";
-//#endif
-// rd.estimate(rgd, 0, CHOLTOL, model,
-// input_var.getInteraction(), input_var.getNgpreds(),
-// invvarmatrix, input_var.getRobust());
-//
-//#if DEBUG
-// cout << "rd.beta\n";
-// rd.beta.print();
-// cout << rd.chi2_score << " <-chi2_scoren\n";
-// cout << "rd.covariance\n";
-// rd.covariance.print();
-// cout << "rd.residuals\n";
-// rd.residuals.print();
-// cout << "rd.sebeta\n";
-// rd.sebeta.print();
-// cout << rd.loglik << " <-logliken\n";
-// cout << rd.sigma2 << " <-sigma2\n";
-//#endif
-// //cout << (rgd.get_unmasked_data()).nids << " 4\n";
-// //}
-// //else
-// //{
-// // rd.mmscore(rgd, 0, CHOLTOL, model,
-// // input_var.getInteraction(),
-// // input_var.getNgpreds(), invvarmatrix);
-// //}
-// }
-//#elif COXPH
-// coxph_reg rd(rgd);
-// rd.estimate(rgd, 0, MAXITER, EPS, CHOLTOL, model,
-// input_var.getInteraction(), true,
-// input_var.getNgpreds());
-//#endif
-//
-// if (!input_var.getAllcov() && input_var.getInteraction() == 0)
-// {
-// start_pos = rd.beta.nrow - 1;
-// } else if (!input_var.getAllcov()
-// && input_var.getInteraction() != 0)
-// {
-// start_pos = rd.beta.nrow - 2;
-// } else
-// {
-// start_pos = 0;
-// }
-//#if DEBUG
-// cout << " start_pos;" << start_pos << "\n";
-//#endif
-// for (int pos = start_pos; pos < rd.beta.nrow; pos++)
-// {
-// *beta_sebeta[0] << input_var.getSep()
-// << rd.beta[pos]
-// << input_var.getSep()
-// << rd.sebeta[pos];
-// //Han Chen
-//#if !COXPH
-// if (input_var.getInverseFilename() == NULL
-// && !input_var.getAllcov()
-// && input_var.getInteraction() != 0)
-// {
-// if (pos > start_pos)
-// {
-// *covvalue[0] << rd.covariance[pos - 1];
-// }
-// }
-//#endif
-// //Oct 26, 2009
-// }
-//
-// //calculate chi2
-// //________________________________
-// if (input_var.getInverseFilename() == NULL)
-// {
-//#if DEBUG
-// cout << " inverse_filename == NULL" << "\n";
-//#endif
-// if (input_var.getScore() == 0)
-// {
-// *chi2[0] << rd.loglik; //2.*(rd.loglik-null_loglik);
-// } else
-// {
-// *chi2[0] << "nan"; //rd.chi2_score;
-// }
-// }
-// //________________________________
-// } else //beta, sebeta = nan
-// {
-// if (!input_var.getAllcov() && input_var.getInteraction() == 0)
-// start_pos = rgd.X.ncol - 1;
-// else if (!input_var.getAllcov()
-// && input_var.getInteraction() != 0)
-// start_pos = rgd.X.ncol - 2;
-// else
-// start_pos = 0;
-//
-// end_pos = rgd.X.ncol;
-// if (input_var.getInteraction() != 0)
-// {
-// end_pos++;
-// }
-// if (input_var.getInteraction() != 0 && !input_var.getAllcov())
-// {
-// start_pos++;
-// }
-//
-// for (int pos = start_pos; pos < end_pos; pos++)
-// {
-// *beta_sebeta[0] << input_var.getSep()
-// << "nan"
-// << input_var.getSep()
-// << "nan";
-// }
-// if (input_var.getInverseFilename() == NULL)
-// {
-// //Han Chen
-//#if !COXPH
-// if (!input_var.getAllcov()
-// && input_var.getInteraction() != 0)
-// {
-// *covvalue[0] << "nan";
-// }
-//#endif
-// //Oct 26, 2009
-// *chi2[0] << "nan";
-// }
-// }
-//
-// if (input_var.getInverseFilename() == NULL)
-// {
-// //Han Chen
-// *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
-//#if !COXPH
-// if (!input_var.getAllcov() && input_var.getInteraction() != 0)
-// {
-// *outfile[0] << covvalue[0]->str() << input_var.getSep();
-// }
-//#endif
-// *outfile[0] << chi2[model]->str() << "\n";
-// //Oct 26, 2009
-// } else
-// {
-// *outfile[0] << beta_sebeta[0]->str() << "\n";
-//#if DEBUG
-// cout << "Se beta" << beta_sebeta[0] << "\n";
-//#endif
-// }
-// }
-//
-//End of Only additive model.
-//
//clean chi2
for (int i = 0; i < 5; i++)
{
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