public double permutePval(
int sLength, int tLength, int nperms, double threshold, HashMap<String, Double> dataIn) {
int count = 0;
for (int i = 0; i < nperms; i++) {
HashSet<String> sgenes = permute.getPermGenes(sLength);
HashSet<String> tgenes = permute.getPermGenes(tLength);
HashSet<String> source = pathwayOverlap(sgenes, geneSet);
HashSet<String> target = pathwayOverlap(tgenes, geneSet);
double sim = geneSetSim(source, target, dataIn);
if (sim > threshold) {
count++;
}
}
return count * 1.0 / nperms;
}
/**
* calculate the p value using the genes all in dif expressed genes
*
* @param snum
* @param tnum
* @param source
* @param perms
* @param threshold
* @param data
* @return
*/
public double pvalCalculationAllInDif(
int snum,
int tnum,
HashSet<String> source,
int perms,
double threshold,
HashMap<String, Double> data) {
double p = 0.0, fenzi = 1.0;
for (int i = 0; i < nperms; i++) {
HashSet<String> rsgenes = permute.getPermGenes(snum, source);
HashSet<String> rtgenes = permute.getPermGenes(tnum, source);
double sim = geneSetSim(rsgenes, rtgenes, data);
if (sim > threshold) {
fenzi += 1;
}
}
p = fenzi / nperms;
return p;
}
/**
* Calculate the p value using the permute label method
*
* @param snum
* @param tnum
* @param union
* @param nperms
* @param thre
* @param data
* @return
*/
public double pValuePermuteLabel(
int snum,
int tnum,
HashSet<String> union,
int nperms,
double thre,
HashMap<String, Double> data) {
double p = 0.0, fenzi = 1.0;
for (int i = 0; i < nperms; i++) {
HashMap<String, HashSet<String>> map = permute.getPermGenes(union, snum, tnum);
double sim =
geneSetSim(
pathwayOverlap(map.get("source"), geneSet),
pathwayOverlap(map.get("target"), geneSet),
data);
if (sim > thre) {
fenzi += 1.0;
}
}
p = fenzi / nperms;
return p;
}
