/**
* Deprecated.
*
* @param rankarray double[]
* @return double[]
*/
private double[] getRanks(double[] rankarray) {
double[] sortdata = new double[data.length];
System.arraycopy(data, 0, sortdata, 0, data.length);
Arrays.sort(sortdata);
int neg = 0;
while ((neg < sortdata.length) && (sortdata[neg] < 0)) {
neg++;
}
int ct = 0;
if (neg > 0) {
for (int i = neg; i > 0; i--) {
rankarray[ct] = -1 * i;
ct++;
}
}
for (int i = 1; ct < rankarray.length; i++) {
rankarray[ct] = i;
ct++;
}
double[] orig_ranks = new double[(int) (segInfo.getEnd() - segInfo.getStart())];
int count = 0;
for (int i = (int) segInfo.getStart(); i < segInfo.getEnd(); i++) {
int index = Arrays.binarySearch(sortdata, (data[i]));
orig_ranks[count] = rankarray[index];
count++;
}
return orig_ranks;
}
/** Performs sign significance test. */
public void runSignTest() {
// System.out.println("In SigTestThread runSignTest()");
float thresh = getThreshhold(data);
int totalbeats = 0;
int overbeats = 0;
int underbeats = 0;
float pval_over = 1;
float pval_under = 1;
// System.out.println("thresh: " + thresh + ", data.length: " + data.length +
// ", segInfo.getStart():" + segInfo.getStart() + ", segInfo.getEnd(): " + segInfo.getEnd());
for (int i = (int) segInfo.getStart(); i <= (int) segInfo.getEnd(); i++) {
if (data[i] > thresh) {
totalbeats++;
overbeats++;
}
if (data[i] < -1 * thresh) {
totalbeats++;
underbeats++;
}
}
if (totalbeats > 15) {
pval_over =
1
- Statistics.getNormalCDF(
(2 * overbeats - totalbeats) / (float) Math.pow(totalbeats, .5));
pval_under =
1
- Statistics.getNormalCDF(
(2 * underbeats - totalbeats) / (float) Math.pow(totalbeats, .5));
} else if (totalbeats > 0) {
pval_over = (float) (1 - Statistics.getBinomialCDF(overbeats, totalbeats));
pval_under = (float) (1 - Statistics.getBinomialCDF(underbeats, totalbeats));
} else {
pval_over = pval_under = 1;
}
segInfo.setStatistic(new String("Sign pos"), pval_over);
segInfo.setStatistic(new String("Sign neg"), pval_under);
// System.out.println("SegmentInfo ["+start+" , "+end+"]: sign p-values: over = "+pval_over+",
// under = "+pval_under);
// put pvalues into chromosomes for storage here?
}
/** Deprecated. */
public void runPermuteTestOld() {
int mean_beats = 0;
int windowsize = (int) (segInfo.getEnd() - segInfo.getStart() + 1);
// gets statistics of the actual segInfo
float realmean = Statistics.getMean(data, (int) segInfo.getStart(), (int) segInfo.getEnd());
orig_mean = realmean;
// copies the data into an array that will be randomized
float[] random_data = new float[data.length];
System.arraycopy(data, 0, random_data, 0, data.length);
boolean precision_reached = false;
segInfo.setNumPermutations(0);
permuteloop:
for (curr_permutation = 0;
(curr_permutation < NUM_PERMUTATIONS && !precision_reached);
curr_permutation++) {
if (stop) {
break permuteloop;
}
// shuffle the array of randomly ordered genes, and ranks if needed
for (int j = random_data.length - 1; j > 0; j--) {
int random_index = (int) (Math.random() * j);
float temp = random_data[random_index];
random_data[random_index] = random_data[j];
random_data[j] = temp;
}
boolean meanbeat = false;
int curr_start = 0;
while ((curr_start < data.length - windowsize) && !meanbeat) {
// sets random statistics ---------------------------
double random_mean = Statistics.getMean(random_data, curr_start, (curr_start + windowsize));
// checks to see if statistics are beat by random--------
if ((!meanbeat)
&& (((realmean > 0) && (random_mean > realmean))
|| ((realmean < 0) && (random_mean < realmean)))) {
mean_beats++;
meanbeat = true;
}
curr_start++;
}
if (mean_beats > PRECISION_THRESH) {
precision_reached = true;
curr_permutation = NUM_PERMUTATIONS;
}
segInfo.setNumPermutations(segInfo.getNumPermutations() + 1);
}
int num_permutations_performed = segInfo.getNumPermutations();
segInfo.setStatistic(
new String("Mean"), (float) mean_beats / (float) num_permutations_performed);
segInfo.setDataMean(orig_mean);
}
/** Actually runs permutation test- for threaded run, use start(). */
public void runPermuteTest() {
// System.out.println("In SigTestThread runPermuteTest()");
float realmean = Statistics.getMean(data, (int) segInfo.getStart(), (int) segInfo.getEnd());
orig_mean = realmean;
int windowsize = (int) (segInfo.getEnd() - segInfo.getStart() + 1);
float[] random_data = new float[data.length];
System.arraycopy(data, 0, random_data, 0, data.length);
float[] random_maxmeans = new float[this.NUM_PERMUTATIONS];
boolean precision_reached = false;
segInfo.setNumPermutations(0);
int mean_beats = 0;
permuteloop:
for (curr_permutation = 0;
(curr_permutation < NUM_PERMUTATIONS && !precision_reached);
curr_permutation++) {
if (stop) {
break permuteloop;
}
// shuffle the array of randomly ordered genes, and ranks if needed
for (int j = random_data.length - 1; j > 0; j--) {
int random_index = (int) (Math.random() * j);
float temp = random_data[random_index];
random_data[random_index] = random_data[j];
random_data[j] = temp;
}
int curr_start = 0;
float curr_mean = Statistics.getMean(random_data, curr_start, (curr_start + windowsize));
float rand_max = 0;
while ((curr_start < Math.min(data.length - windowsize, this.MAX_PERMUTE_VAL))) {
curr_mean -= random_data[curr_start] / windowsize;
curr_mean += random_data[curr_start + windowsize] / windowsize;
if (curr_mean < 0 && curr_mean < rand_max) rand_max = curr_mean;
else if (curr_mean > 0 && curr_mean > rand_max) rand_max = curr_mean;
curr_start++;
}
random_maxmeans[curr_permutation] = rand_max;
if (((realmean > 0) && (rand_max > realmean)) || ((realmean < 0) && (rand_max < realmean)))
mean_beats++;
if (mean_beats > PRECISION_THRESH) precision_reached = true;
}
segInfo.setNumPermutations(curr_permutation);
segInfo.setDataMean(orig_mean);
float maxMean = Statistics.getMean(random_maxmeans, 0, curr_permutation - 1);
float maxVar = Statistics.getVariance(random_maxmeans, 0, curr_permutation - 1, maxMean);
float pvalue = 1;
if (realmean > 0)
pvalue = 1 - Statistics.getNormalCDF((realmean - maxMean) / (float) Math.pow(maxVar, .5));
else pvalue = Statistics.getNormalCDF((realmean - maxMean) / (float) Math.pow(maxVar, .5));
segInfo.setStatistic(new String("Mean"), pvalue);
}