CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
string helpString = "";
helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n";
helpString += "If you provide a metadata file, mothur will calculate te correlation bewteen the metadata and the otus.\n";
- helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method and label. The shared or relabund parameter is required.\n";
+ helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method, cutoff and label. The shared or relabund parameter is required.\n";
helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n";
+ helpString += "The cutoff parameter allows you to set a pvalue at which the otu will be reported.\n";
helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n";
helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n";
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
+ string temp = validParameter.validFile(parameters, "cutoff", false);
+ if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, cutoff);
+
if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
}
else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}