edu.cmu.tetradapp.model.YeastPcCcdSearchWrapper Maven / Gradle / Ivy
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///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// 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 //
// the Free Software Foundation; either version 2 of the License, or //
// (at your option) any later version. //
// //
// This program is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
// along with this program; if not, write to the Free Software //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetradapp.model;
//package
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.data.SimpleDataLoader;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.Ccd;
import edu.cmu.tetrad.search.Pc;
import edu.cmu.tetrad.search.work_in_progress.IndTestCramerT;
import edu.pitt.dbmi.data.reader.Delimiter;
import java.io.DataOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
/**
* This version (in the urchin/newdata directory) differs from the version in
* the batchsearch directory. It will create both a doc file and an xls file. The latter corresponds to the "verbose =
* false" segments of the earlier version. Also this version will deal with the situation where there are many time
* steps, which raises question about the time interval used to decide whether there is an adjacency between two
* variables (= gene/time pairs).
*
Also all the GA code has been removed.
*
* @author josephramsey
* @version $Id: $Id
*/
public class YeastPcCcdSearchWrapper {
/**
*
main.
*
* @param args an array of {@link java.lang.String} objects
*/
public static void main(String[] args) {
int[][] yeastReg = {{1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0},
{0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0},
{1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1},
{0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1},
{0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0},
{0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0},
{0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1},
{0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0},
{0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1},
{1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0},
{0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1}};
List listOfNames = new ArrayList<>();
// get the file containing the file names
DataSet cds = null;
try {
cds = SimpleDataLoader.loadContinuousData(new File(args[0]), "//", '\"',
"*", true, Delimiter.TAB, false);
} catch (IOException e) {
e.printStackTrace();
}
String outfileprefix = args[1];
String outverbosefile = outfileprefix + ".doc";
String outsummaryfile = outfileprefix + ".xls";
OutputStream s1 = null;
OutputStream s2 = null;
try {
s1 = Files.newOutputStream(Paths.get(outverbosefile));
} catch (IOException e) {
System.out.println("Cannot open file file " + outverbosefile);
System.exit(0);
}
DataOutputStream d1 = new DataOutputStream(s1);
try {
s2 = Files.newOutputStream(Paths.get(outsummaryfile));
} catch (IOException e) {
System.out.println("Cannot open file file " + outsummaryfile);
System.exit(0);
}
DataOutputStream d2 = new DataOutputStream(s2);
try {
//if(!verbose) {
d2.writeBytes(
"File\tPC05 FP\tPC05 FN\tPC10 FP\tPC10 FN\tPC15 FP\t");
d2.writeBytes("PC15 FN\tPC20 FP\tPC20 FN\tPC30 FP\tPC30 FN\t");
d2.writeBytes(
"CCD05 FP\tCCD05 FN\tCCD10 FP\tCCD10 FN\tCCD 15 FP\t");
d2.writeBytes(
"CCD15 FN\tCCD20 FP\tCCD20 FN\tCCD30 FP\tCCD 30 FN\n");
//}
// read in variable name and set up DataSet.
int ngenes = Integer.parseInt(args[2]);
Knowledge bk = new Knowledge();
bk.addToTiersByVarNames(listOfNames);
//if(verbose) {
d1.writeBytes("\n \n**Results for data in file yeastTRN**\n \n");
d1.writeBytes(" Acutal adj matrix: \n");
YeastPcCcdSearchWrapper.printAdjMatrix(yeastReg, listOfNames, d1);
//}
int[] PC05Accuracy;
PC05Accuracy = YeastPcCcdSearchWrapper.PCAccuracy(0.05, ngenes, cds, bk, yeastReg,
listOfNames, d1);
int[] PC10Accuracy;
PC10Accuracy = YeastPcCcdSearchWrapper.PCAccuracy(0.10, ngenes, cds, bk, yeastReg,
listOfNames, d1);
int[] PC15Accuracy;
PC15Accuracy = YeastPcCcdSearchWrapper.PCAccuracy(0.15, ngenes, cds, bk, yeastReg,
listOfNames, d1);
int[] PC20Accuracy;
PC20Accuracy = YeastPcCcdSearchWrapper.PCAccuracy(0.20, ngenes, cds, bk, yeastReg,
listOfNames, d1);
int[] PC30Accuracy;
PC30Accuracy = YeastPcCcdSearchWrapper.PCAccuracy(0.30, ngenes, cds, bk, yeastReg,
listOfNames, d1);
int[] CCD05Accuracy;
CCD05Accuracy = YeastPcCcdSearchWrapper.CcdAccuracy(0.05, ngenes, cds, yeastReg,
listOfNames, d1);
int[] CCD10Accuracy;
CCD10Accuracy = YeastPcCcdSearchWrapper.CcdAccuracy(0.10, ngenes, cds, yeastReg,
listOfNames, d1);
int[] CCD15Accuracy;
CCD15Accuracy = YeastPcCcdSearchWrapper.CcdAccuracy(0.15, ngenes, cds, yeastReg,
listOfNames, d1);
int[] CCD20Accuracy;
CCD20Accuracy = YeastPcCcdSearchWrapper.CcdAccuracy(0.20, ngenes, cds, yeastReg,
listOfNames, d1);
int[] CCD30Accuracy;
CCD30Accuracy = YeastPcCcdSearchWrapper.CcdAccuracy(0.30, ngenes, cds, yeastReg,
listOfNames, d1);
//if(!verbose) {
d2.writeBytes("yeastTRN \t");
d2.writeBytes(PC05Accuracy[0] + "\t");
d2.writeBytes(PC05Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(PC10Accuracy[0] + "\t");
d2.writeBytes(PC10Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(PC15Accuracy[0] + "\t");
d2.writeBytes(PC15Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(PC20Accuracy[0] + "\t");
d2.writeBytes(PC20Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(PC30Accuracy[0] + "\t");
d2.writeBytes(PC30Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(CCD05Accuracy[0] + "\t");
d2.writeBytes(CCD05Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(CCD10Accuracy[0] + "\t");
d2.writeBytes(CCD10Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(CCD15Accuracy[0] + "\t");
d2.writeBytes(CCD15Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(CCD20Accuracy[0] + "\t");
d2.writeBytes(CCD20Accuracy[1] + "\t");
//}
//if(!verbose) {
d2.writeBytes(CCD30Accuracy[0] + "\t");
d2.writeBytes(CCD30Accuracy[1] + "\n");
//}
} catch (Exception e) {
e.printStackTrace();
}
}
private static int[] CcdAccuracy(double alpha, int ngenes,
DataSet cds, int[][] yeastReg, List names,
DataOutputStream d) {
int[] falsePosNeg = new int[2];
IndTestCramerT indTestCramerT = new IndTestCramerT(cds, alpha);
Ccd ccd = new Ccd(indTestCramerT);
Graph ccdModel = null;
try {
ccdModel = ccd.search();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
int falsePositives = 0;
int falseNegatives = 0;
int[][] ccdModelAdj = new int[ngenes][ngenes];
int nvariables = names.size();
for (int i = 0; i < nvariables; i++) {
String namei = names.get(i);
for (int j = 0; j < nvariables; j++) {
String namej = names.get(j);
ccdModelAdj[i][j] = 0;
Node vari = indTestCramerT.getVariable(namei);
Node varj = indTestCramerT.getVariable(namej);
if (!ccdModel.isAdjacentTo(vari, varj)) {
continue;
}
ccdModelAdj[i][j] = 1;
}
}
for (int i = 0; i < ngenes; i++) {
for (int j = i; j < ngenes; j++) {
if (yeastReg[i][j] == 0 && ccdModelAdj[i][j] == 1) {
falsePositives++;
}
if (yeastReg[i][j] == 1 && ccdModelAdj[i][j] == 0) {
falseNegatives++;
}
}
}
falsePosNeg[0] = falsePositives;
falsePosNeg[1] = falseNegatives;
try {
d.writeBytes("\n \n");
d.writeBytes(" Results of CCD search with alpha = " + alpha);
d.writeBytes(" false+ " + falsePositives + "\t");
d.writeBytes("false- " + falseNegatives + "\n");
d.writeBytes(" Adjacency matrix of estimated model: \n");
} catch (Exception e) {
e.printStackTrace();
}
YeastPcCcdSearchWrapper.printAdjMatrix(ccdModelAdj, names, d);
return falsePosNeg;
}
private static int[] PCAccuracy(double alpha, int ngenes,
DataSet cds, Knowledge bk, int[][] yeastReg, List names,
DataOutputStream d) {
int[] falsePosNeg = new int[2];
IndTestCramerT indTestCramerT = new IndTestCramerT(cds, alpha);
Pc pcs = new Pc(indTestCramerT);
pcs.setKnowledge(bk);
Graph pcModel = null;
try {
pcModel = pcs.search();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
int falsePositives = 0;
int falseNegatives = 0;
int[][] pcModelAdj = new int[ngenes][ngenes];
int nvariables = names.size();
// int ntimes = nvariables / ngenes;
for (int i = 0; i < nvariables; i++) {
String namei = names.get(i);
for (int j = 0; j < nvariables; j++) {
String namej = names.get(j);
pcModelAdj[i][j] = 0;
Node vari = indTestCramerT.getVariable(namei);
Node varj = indTestCramerT.getVariable(namej);
if (!pcModel.isAdjacentTo(vari, varj)) {
continue;
}
pcModelAdj[i][j] = 1;
}
}
for (int i = 0; i < ngenes; i++) {
for (int j = i; j < ngenes; j++) {
if (yeastReg[i][j] == 0 && pcModelAdj[i][j] == 1) {
falsePositives++;
}
if (yeastReg[i][j] == 1 && pcModelAdj[i][j] == 0) {
falseNegatives++;
}
}
}
falsePosNeg[0] = falsePositives;
falsePosNeg[1] = falseNegatives;
try {
d.writeBytes("\n \n");
d.writeBytes(" Results of PC search with alpha = " + alpha);
d.writeBytes(" false+ " + falsePositives + "\t");
d.writeBytes("false- " + falseNegatives + "\n");
d.writeBytes(" Adjacency matrix of estimated model: \n");
} catch (Exception e) {
e.printStackTrace();
}
YeastPcCcdSearchWrapper.printAdjMatrix(pcModelAdj, names, d);
return falsePosNeg;
}
private static void printAdjMatrix(int[][] adjMat, List listOfNames,
DataOutputStream d) {
for (int i = 0; i < adjMat.length; i++) {
try {
d.writeBytes(" " + listOfNames.get(i) + "\t");
for (int j = 0; j <= i; j++) {
d.writeBytes(adjMat[i][j] + "\t");
}
d.writeBytes("\n");
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
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