[Genabel-commits] r1127 - pkg/ProbABEL/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 10 22:21:22 CET 2013
Author: maartenk
Date: 2013-03-10 22:21:22 +0100 (Sun, 10 Mar 2013)
New Revision: 1127
Modified:
pkg/ProbABEL/src/main.cpp
Log:
ProbABEL output should be identical to output before revision 1122
Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp 2013-03-10 17:38:00 UTC (rev 1126)
+++ pkg/ProbABEL/src/main.cpp 2013-03-10 21:21:22 UTC (rev 1127)
@@ -58,15 +58,19 @@
{
if (csnp == 0)
{
- std::cout << "Analysis: " << setw(5)
+ std::cout << "Analysis: "
+ << setw(5)
<< 100. * static_cast<double>(csnp)
- / static_cast<double>(nsnps) << "%...";
+ / static_cast<double>(nsnps)
+ << "%...";
} else
{
- std::cout << "\b\b\b\b\b\b\b\b\b" << setw(5)
+ std::cout << "\b\b\b\b\b\b\b\b\b"
+ << setw(5)
<< 100. * static_cast<double>(csnp)
- / static_cast<double>(nsnps) << "%...";
+ / static_cast<double>(nsnps)
+ << "%...";
}
std::cout.flush();
}
@@ -90,7 +94,8 @@
outfile[i]->open((filenames[i]).c_str());
if (!outfile[i]->is_open())
{
- std::cerr << "Cannot open file for writing: " << filenames[i]
+ std::cerr << "Cannot open file for writing: "
+ << filenames[i]
<< "\n";
exit(1);
}
@@ -113,7 +118,9 @@
|| interaction_cox > phd.ncov)
{
std::cerr << "error: Interaction parameter is out of range "
- << "(interaction=" << input_var.getInteraction() << ") \n";
+ << "(interaction="
+ << input_var.getInteraction()
+ << ") \n";
exit(1);
}
@@ -135,11 +142,22 @@
{
for (unsigned int i = 0; i < outfile.size(); i++)
{
- (*outfile[i]) << "name" << input_var.getSep() << "A1"
- << input_var.getSep() << "A2" << input_var.getSep() << "Freq1"
- << input_var.getSep() << "MAF" << input_var.getSep()
- << "Quality" << input_var.getSep() << "Rsq"
- << input_var.getSep() << "n" << input_var.getSep()
+ (*outfile[i]) << "name"
+ << input_var.getSep()
+ << "A1"
+ << input_var.getSep()
+ << "A2"
+ << input_var.getSep()
+ << "Freq1"
+ << input_var.getSep()
+ << "MAF"
+ << input_var.getSep()
+ << "Quality"
+ << input_var.getSep()
+ << "Rsq"
+ << input_var.getSep()
+ << "n"
+ << input_var.getSep()
<< "Mean_predictor_allele";
if (input_var.getChrom() != "-1")
(*outfile[i]) << input_var.getSep() << "chrom";
@@ -151,8 +169,11 @@
{
for (unsigned int file = 0; file < outfile.size(); file++)
for (int i = 0; i < phd.n_model_terms - 1; i++)
- *outfile[file] << input_var.getSep() << "beta_"
- << phd.model_terms[i] << input_var.getSep() << "sebeta_"
+ *outfile[file] << input_var.getSep()
+ << "beta_"
+ << phd.model_terms[i]
+ << input_var.getSep()
+ << "sebeta_"
<< phd.model_terms[i];
}
}
@@ -162,32 +183,53 @@
{
create_start_of_header(outfile, input_var, phd);
- *outfile[0] << input_var.getSep() << "beta_SNP_A1A2" << input_var.getSep()
- << "beta_SNP_A1A1" << input_var.getSep() << "sebeta_SNP_A1A2"
- << input_var.getSep() << "sebeta_SNP_A1A1";
+ *outfile[0] << input_var.getSep()
+ << "beta_SNP_A1A2"
+ << input_var.getSep()
+ << "beta_SNP_A1A1"
+ << input_var.getSep()
+ << "sebeta_SNP_A1A2"
+ << input_var.getSep()
+ << "sebeta_SNP_A1A1";
- *outfile[1] << input_var.getSep() << "beta_SNP_addA1" << input_var.getSep()
+ *outfile[1] << input_var.getSep()
+ << "beta_SNP_addA1"
+ << input_var.getSep()
<< "sebeta_SNP_addA1";
- *outfile[2] << input_var.getSep() << "beta_SNP_domA1" << input_var.getSep()
+ *outfile[2] << input_var.getSep()
+ << "beta_SNP_domA1"
+ << input_var.getSep()
<< "sebeta_SNP_domA1";
- *outfile[3] << input_var.getSep() << "beta_SNP_recA1" << input_var.getSep()
+ *outfile[3] << input_var.getSep()
+ << "beta_SNP_recA1"
+ << input_var.getSep()
<< "sebeta_SNP_recA1";
- *outfile[4] << input_var.getSep() << "beta_SNP_odom" << input_var.getSep()
+ *outfile[4] << input_var.getSep()
+ << "beta_SNP_odom"
+ << input_var.getSep()
<< "sebeta_SNP_odom";
if (input_var.getInteraction() != 0)
{
//Han Chen
- *outfile[0] << input_var.getSep() << "beta_SNP_A1A2_"
- << phd.model_terms[interaction_cox] << input_var.getSep()
- << "sebeta_SNP_A1A2_" << phd.model_terms[interaction_cox]
- << input_var.getSep() << "beta_SNP_A1A1_"
- << phd.model_terms[interaction_cox] << input_var.getSep()
- << "sebeta_SNP_A1A1_" << phd.model_terms[interaction_cox];
+ *outfile[0] << input_var.getSep()
+ << "beta_SNP_A1A2_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
+ << "sebeta_SNP_A1A2_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
+ << "beta_SNP_A1A1_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
+ << "sebeta_SNP_A1A1_"
+ << phd.model_terms[interaction_cox];
#if !COXPH
if (input_var.getInverseFilename() == NULL && !input_var.getAllcov())
{
- *outfile[0] << input_var.getSep() << "cov_SNP_A1A2_int_SNP_"
- << phd.model_terms[interaction_cox] << input_var.getSep()
+ *outfile[0] << input_var.getSep()
+ << "cov_SNP_A1A2_int_SNP_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
<< "cov_SNP_A1A1_int_SNP_"
<< phd.model_terms[interaction_cox];
}
@@ -195,15 +237,19 @@
//Oct 26, 2009
for (unsigned int file = 1; file < outfile.size(); file++)
{
- *outfile[file] << input_var.getSep() << "beta_SNP_"
- << phd.model_terms[interaction_cox] << input_var.getSep()
- << "sebeta_SNP_" << phd.model_terms[interaction_cox];
+ *outfile[file] << input_var.getSep()
+ << "beta_SNP_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
+ << "sebeta_SNP_"
+ << phd.model_terms[interaction_cox];
//Han Chen
#if !COXPH
if (input_var.getInverseFilename() == NULL
&& !input_var.getAllcov())
{
- *outfile[file] << input_var.getSep() << "cov_SNP_int_SNP_"
+ *outfile[file] << input_var.getSep()
+ << "cov_SNP_int_SNP_"
<< phd.model_terms[interaction_cox];
}
#endif
@@ -221,14 +267,19 @@
phedata& phd, int interaction_cox)
{
create_start_of_header(outfile, input_var, phd);
- *outfile[0] << input_var.getSep() << "beta_SNP_add" << input_var.getSep()
+ *outfile[0] << input_var.getSep()
+ << "beta_SNP_add"
+ << input_var.getSep()
<< "sebeta_SNP_add";
if (input_var.getInteraction() != 0)
{
- *outfile[0] << input_var.getSep() << "beta_SNP_"
- << phd.model_terms[interaction_cox] << input_var.getSep()
- << "sebeta_SNP_" << phd.model_terms[interaction_cox];
+ *outfile[0] << input_var.getSep()
+ << "beta_SNP_"
+ << phd.model_terms[interaction_cox]
+ << input_var.getSep()
+ << "sebeta_SNP_"
+ << phd.model_terms[interaction_cox];
}
if (input_var.getInverseFilename() == NULL)
@@ -237,7 +288,8 @@
#if !COXPH
if (input_var.getInteraction() != 0 && !input_var.getAllcov())
{
- *outfile[0] << input_var.getSep() << "cov_SNP_int_SNP_"
+ *outfile[0] << input_var.getSep()
+ << "cov_SNP_int_SNP_"
<< phd.model_terms[interaction_cox];
}
#endif
@@ -251,12 +303,23 @@
const mlinfo& mli, int csnp, const cmdvars& input_var, int gcount,
double freq)
{
- *outfile[file] << mli.name[csnp] << input_var.getSep() << mli.A1[csnp]
- << input_var.getSep() << mli.A2[csnp] << input_var.getSep()
- << mli.Freq1[csnp] << input_var.getSep() << mli.MAF[csnp]
- << input_var.getSep() << mli.Quality[csnp] << input_var.getSep()
- << mli.Rsq[csnp] << input_var.getSep() << gcount
- << input_var.getSep() << freq;
+ *outfile[file] << mli.name[csnp]
+ << input_var.getSep()
+ << mli.A1[csnp]
+ << input_var.getSep()
+ << mli.A2[csnp]
+ << input_var.getSep()
+ << mli.Freq1[csnp]
+ << input_var.getSep()
+ << mli.MAF[csnp]
+ << input_var.getSep()
+ << mli.Quality[csnp]
+ << input_var.getSep()
+ << mli.Rsq[csnp]
+ << input_var.getSep()
+ << gcount
+ << input_var.getSep()
+ << freq;
if (input_var.getChrom() != "-1")
{
*outfile[file] << input_var.getSep() << input_var.getChrom();
@@ -403,7 +466,8 @@
if (!outfile[0]->is_open())
{
- std::cerr << "Cannot open file for writing: " << outfilename_str
+ std::cerr << "Cannot open file for writing: "
+ << outfilename_str
<< "\n";
exit(1);
}
@@ -605,7 +669,8 @@
for (int pos = start_pos; pos < rd.beta.nrow; pos++)
{
*beta_sebeta[model] << input_var.getSep()
- << rd.beta[pos] << input_var.getSep()
+ << rd.beta[pos]
+ << input_var.getSep()
<< rd.sebeta[pos];
//Han Chen
#if !COXPH
@@ -620,8 +685,8 @@
if (pos > start_pos + 2
|| input_var.getNgpreds() != 2)
{
- *covvalue[model]
- << rd.covariance[pos - 3]
+ *covvalue[model] << rd.covariance[pos
+ - 3]
<< input_var.getSep()
<< rd.covariance[pos - 2];
}
@@ -637,10 +702,16 @@
//calculate chi2
//________________________________
- if (input_var.getInverseFilename() == NULL
+ //cout << rd.loglik<<" "<<input_var.getNgpreds() << "\n";
+
+ if ((input_var.getInverseFilename() == NULL
&& input_var.getNgpreds() != 2)
+ || input_var.getNgpreds() == 2)
{
-
+ cout << rd.loglik
+ << " "
+ << input_var.getNgpreds()
+ << "\n";
if (input_var.getScore() == 0)
{
//*chi2[model] << 2.*(rd.loglik-null_loglik);
@@ -708,8 +779,10 @@
for (int pos = start_pos; pos < end_pos; pos++)
{
- *beta_sebeta[model] << input_var.getSep() << "nan"
- << input_var.getSep() << "nan";
+ *beta_sebeta[model] << input_var.getSep()
+ << "nan"
+ << input_var.getSep()
+ << "nan";
}
if (input_var.getNgpreds() == 2)
@@ -721,7 +794,8 @@
{
if (model == 0)
{
- *covvalue[model] << "nan" << input_var.getSep()
+ *covvalue[model] << "nan"
+ << input_var.getSep()
<< "nan";
} else
{
@@ -749,85 +823,81 @@
}
}
- //end of model cycle
- if (input_var.getNgpreds() == 2)
+ }
+ //end of model cycle
+ if (input_var.getNgpreds() == 2)
+ {
+ cout << "ngpreds==2 model end" << "\n";
+
+ //Han Chen
+ *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
+#if !COXPH
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
{
- //Han Chen
- *outfile[0] << beta_sebeta[0]->str() << input_var.getSep();
+ *outfile[0] << covvalue[0]->str() << input_var.getSep();
+ }
+#endif
+ *outfile[0] << chi2[0]->str() << "\n";
+
+ *outfile[1] << beta_sebeta[1]->str() << input_var.getSep();
#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *outfile[0] << covvalue[0]->str() << input_var.getSep();
- }
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[1] << covvalue[1]->str() << input_var.getSep();
+ }
#endif
- *outfile[0] << chi2[0]->str() << "\n";
+ *outfile[1] << chi2[1]->str() << "\n";
- *outfile[1] << beta_sebeta[1]->str() << input_var.getSep();
+ *outfile[2] << beta_sebeta[2]->str() << input_var.getSep();
#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *outfile[1] << covvalue[1]->str() << input_var.getSep();
- }
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[2] << covvalue[2]->str() << input_var.getSep();
+ }
#endif
- *outfile[1] << chi2[1]->str() << "\n";
+ *outfile[2] << chi2[2]->str() << "\n";
- *outfile[2] << beta_sebeta[2]->str() << input_var.getSep();
+ *outfile[3] << beta_sebeta[3]->str() << input_var.getSep();
#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *outfile[2] << covvalue[2]->str() << input_var.getSep();
- }
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[3] << covvalue[3]->str() << input_var.getSep();
+ }
#endif
- *outfile[2] << chi2[2]->str() << "\n";
+ *outfile[3] << chi2[3]->str() << "\n";
- *outfile[3] << beta_sebeta[3]->str() << input_var.getSep();
+ *outfile[4] << beta_sebeta[4]->str() << input_var.getSep();
#if !COXPH
- if (!input_var.getAllcov()
- && input_var.getInteraction() != 0)
- {
- *outfile[3] << covvalue[3]->str() << input_var.getSep();
- }
+ if (!input_var.getAllcov() && input_var.getInteraction() != 0)
+ {
+ *outfile[4] << covvalue[4]->str() << input_var.getSep();
+ }
#endif
- *outfile[3] << chi2[3]->str() << "\n";
+ *outfile[4] << chi2[4]->str() << "\n";
+ //Oct 26, 2009
- *outfile[4] << beta_sebeta[4]->str() << input_var.getSep();
+ } else //ngpreds == 1
+ {
+
+ 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[4] << covvalue[4]->str() << input_var.getSep();
+ *outfile[0] << covvalue[0]->str() << input_var.getSep();
}
#endif
- *outfile[4] << chi2[4]->str() << "\n";
+ *outfile[0] << chi2[0]->str() << "\n";
//Oct 26, 2009
-
- } else //ngpreds == 1
+ } else
{
+ *outfile[0] << beta_sebeta[0]->str() << "\n";
+ }
+ } // end ngpreds ==1
- 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";
- }
- } // end ngpreds ==1
- }
}
//
//End of All models output.
@@ -960,8 +1030,10 @@
#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];
+ *beta_sebeta[0] << input_var.getSep()
+ << rd.beta[pos]
+ << input_var.getSep()
+ << rd.sebeta[pos];
//Han Chen
#if !COXPH
if (input_var.getInverseFilename() == NULL
@@ -1015,8 +1087,10 @@
for (int pos = start_pos; pos < end_pos; pos++)
{
- *beta_sebeta[0] << input_var.getSep() << "nan"
- << input_var.getSep() << "nan";
+ *beta_sebeta[0] << input_var.getSep()
+ << "nan"
+ << input_var.getSep()
+ << "nan";
}
if (input_var.getInverseFilename() == NULL)
{
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