org.snpeff.geneSets.algorithm.EnrichmentAlgorithm Maven / Gradle / Ivy
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Variant annotation and effect prediction package.
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package org.snpeff.geneSets.algorithm;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import org.apfloat.Apfloat;
import org.snpeff.geneSets.GeneSet;
import org.snpeff.geneSets.GeneSets;
import org.snpeff.geneSets.GeneSetsRanked;
import org.snpeff.geneSets.Result;
/**
* A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
*
* @author pcingola
*/
public abstract class EnrichmentAlgorithm {
public enum EnrichmentAlgorithmType {
FISHER_GREEDY, RANKSUM_GREEDY, FISHER, RANKSUM, LEADING_EDGE_FRACTION, NONE;
/**
* Is the algorithm base on "interesting / not-interesting" binary clasification?
* @return
*/
public boolean isBinary() {
return (this == FISHER) || (this == FISHER_GREEDY);
}
/**
* Is this a greedy algorithm?
* @return
*/
public boolean isGreedy() {
return (this == FISHER_GREEDY) || (this == RANKSUM_GREEDY);
}
/**
* Does the algorithm need a rank statistic?
* @return
*/
public boolean isRank() {
return (this == RANKSUM) || (this == RANKSUM_GREEDY);
}
}
public static final int HTML_TD_GENES_MAX_LEN = 40;
public static final String HTML_BG_COLOR[] = { "dddddd", "eeeeee" };
public static final String HTML_BG_COLOR_TITLE = "cccccc";
boolean debug = false;
boolean verbose = false;
boolean htmlTable = false;
int minGeneSetSize = 0;
int maxGeneSetSize = Integer.MAX_VALUE;
int numberToSelect;
double maxPValue = Double.NaN;
double maxPvalueAdjusted = 0.05;
StringBuilder output = new StringBuilder();
GeneSets geneSets;
Set filterOutputGeneSets;
public static long PRINT_SOMETHING_TIME = 5000; // Print something every X milliseconds
public EnrichmentAlgorithm(GeneSets geneSets, int numberToSelect) {
this.geneSets = geneSets;
this.numberToSelect = numberToSelect;
}
public double getMaxPvalueAdjusted() {
return maxPvalueAdjusted;
}
public StringBuilder getOutput() {
return output;
}
/**
* Showld we show this result or should the output be filtered?
* @param result
* @return
*/
protected boolean isShow(Result result) {
// Filter by pValue
if (Double.isNaN(maxPValue)) {
// Use adjusted p-value
if (result.getPvalueAdjusted() >= maxPvalueAdjusted) return false;
} else {
// Use un-adjusted p-value
if (result.getPvalue().doubleValue() >= maxPValue) return false;
}
// Filter by Gene set name (show only if it is in this list)
if (filterOutputGeneSets != null) {
String gsName = result.getLatestGeneSet().getName();
boolean show = filterOutputGeneSets.contains(gsName);
if (verbose) System.err.println("\tFilter output list. Show geneSet '" + gsName + "' : " + show);
return show;
}
// OK
return true;
}
protected void print(String str) {
System.out.println(str);
output.append(str + "\n");
}
/**
* Print after all genesets are shown
*/
void printEnd() {
if (htmlTable) print("");
}
/**
* Show a result
* @param it : Iteration or Rank
* @param result
*/
void printResult(int it, Result result) {
if ((result != null) && (result.getLatestGeneSet() != null)) {
if (isShow(result)) {
GeneSet geneSet = result.getLatestGeneSet();
//---
// Get genes information
//---
StringBuffer interestingGenes = new StringBuffer();
ArrayList genesList = new ArrayList();
genesList.addAll(geneSet.getInterestingGenes());
Collections.sort(genesList);
for (String gene : genesList) {
interestingGenes.append(gene);
// Show score (value) and rank information?
if (geneSets.hasValue(gene) || geneSets.isRanked()) {
interestingGenes.append("[");
// Append value
if (geneSets.hasValue(gene)) interestingGenes.append(geneSets.getValue(gene));
// Append rank
if (geneSets.isRanked()) {
GeneSetsRanked geneSetsRanked = ((GeneSetsRanked) geneSets);
interestingGenes.append("/" + geneSetsRanked.getRank(gene));
}
interestingGenes.append("]");
}
interestingGenes.append(" ");
}
//---
// Print output
//---
if (htmlTable) {
// Show as HTML table
String descr = geneSet.getDescription();
String name = geneSet.getName();
if (descr.startsWith("http://")) {
name = "" + name + "";
descr = "link";
}
String intGenes = interestingGenes.toString();
if (interestingGenes.length() > HTML_TD_GENES_MAX_LEN) intGenes = "";
String bgcolor = HTML_BG_COLOR[it % 2];
print("\t " + it //
+ " \t" + String.format("%.2e", result.getPvalue().doubleValue()) //
+ " \t" + String.format("%.2e", result.getPvalueAdjusted()) //
+ " \t" + name //
+ " \t" + geneSet.size() //
+ " \t" + descr //
+ " \t" + intGenes //
+ " \t" + (geneSets.isRanked() ? geneSet.rankSum() : 0) //
+ " \t ");
} else {
// Show as "normal" TXT
print(it //
+ "\t" + result.getPvalue() //
+ "\t" + result.getPvalueAdjusted() //
+ "\t" + geneSet.getName() //
+ "\t" + geneSet.size() //
+ "\t" + geneSet.getDescription() //
+ "\t" + result.getGeneSets() //
+ "\t" + interestingGenes //
+ "\t" + (geneSets.isRanked() ? geneSet.rankSum() : 0) //
);
}
}
} // else print("\t" + it + "\tNULL");
}
/**
* Print before all genesets are shown
*/
void printTitle() {
if (htmlTable) print(" Rank \tp-value \tp-value adj \tLatest result \tSize \tDescription \tInteresting genes \t Score ");
else if (verbose) print("Iteration\tp-value\tp-value adj\tLatest result\tSize\tDescription\tResult\tInteresting genes");
}
/**
* Calculate the pValue for a given geneSet
* @param geneSetList
* @return
*/
abstract Apfloat pValue(GeneSet geneSet);
/**
* Create a new gene set using all gene sets and calculate pValue
* @param geneSetList
* @return
*/
Apfloat pValue(List geneSetList) {
GeneSet newGeneSet = new GeneSet(geneSetList, geneSets);
return pValue(newGeneSet);
}
/**
* Select the 'best' gene sets
* @return
*/
public Result select() {
Result best = new Result();
//---
// Calculate pValues for each gene set matching our criteria
//---
List results = new ArrayList();
for (GeneSet geneSet : geneSets) {
if ((geneSet.getGeneCount() > 0) // This term is empty? => skip it
&& (geneSet.getGeneCount() >= minGeneSetSize) // Use gene sets bigger than minGeneSetSize
&& (geneSet.getGeneCount() <= maxGeneSetSize) // Use gene sets smaller than maxGeneSetSize
) {
// Calculate pValue
Apfloat pValue = pValue(geneSet);
Result result = new Result(geneSet, pValue, 0); // We'll update the geneSetCount later
results.add(result);
}
}
// Update the geneSetCount
for (Result res : results)
res.setGeneSetCountLast(results.size());
//---
// Show results
//---
if (htmlTable || verbose) {
printTitle();
// Sort by pValue
Collections.sort(results);
// Show them
int rank = 1;
for (Result r : results)
printResult(rank++, r);
printEnd();
}
return best;
}
public void setDebug(boolean debug) {
this.debug = debug;
}
public void setFilterOutputGeneSets(Set filterOutputGeneSets) {
this.filterOutputGeneSets = filterOutputGeneSets;
}
public void setHtmlTable(boolean htmlTable) {
this.htmlTable = htmlTable;
}
public void setMaxGeneSetSize(int maxGeneSetSize) {
this.maxGeneSetSize = maxGeneSetSize;
}
public void setMaxPValue(double maxPValue) {
this.maxPValue = maxPValue;
}
public void setMaxPvalueAdjusted(double maxPvalueAdjusted) {
this.maxPvalueAdjusted = maxPvalueAdjusted;
}
public void setMinGeneSetSize(int minGeneSetSize) {
this.minGeneSetSize = minGeneSetSize;
}
public void setVerbose(boolean verbose) {
this.verbose = verbose;
}
}
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