trans.roc
Class RocWindowScanner

java.lang.Object
  trans.roc.RocWindowScanner

public class RocWindowScanner

extends java.lang.Object

Scans a window array over a range of thresholds and intersects with a list of positives to generate the false positive rate, true positive rate, and false discovery rates.

Constructor Summary

RocWindowScanner(java.lang.String[] args)

Method Summary

double	calcFDR(double threshold) Scans an array of Window intersecting with positives to calculate an FDR at a given threshold.
void	calculateTotalWindowIntersectionStats() Calculate total # windows that intersect pos regions, no counting, ie one window overlaps two pos regions is counted once.
double[]	findStartStopThresholds(double startThreshold, double stopThreshold)
double	findTargetFDRThreshold(double fdrTarget, int maxCycles) Attempts to find a threshold that gives the target FDR, will run through maxCycles and return closest threshold if targetFDR is not reached.
static void	main(java.lang.String[] args)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
void	removeMaskedRegions() Remove windows that intersect the masked regions.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RocWindowScanner

public RocWindowScanner(java.lang.String[] args)

Method Detail

main

public static void main(java.lang.String[] args)

calculateTotalWindowIntersectionStats

public void calculateTotalWindowIntersectionStats()

Calculate total # windows that intersect pos regions, no counting, ie one window overlaps two pos regions is counted once. Also strip out windows that partially overlap a positive region but don't meet the fractionAcceptibleCoverage.

removeMaskedRegions

public void removeMaskedRegions()

Remove windows that intersect the masked regions.

calcFDR

public double calcFDR(double threshold)

Scans an array of Window intersecting with positives to calculate an FDR at a given threshold.

findTargetFDRThreshold

public double findTargetFDRThreshold(double fdrTarget,
                                     int maxCycles)

Attempts to find a threshold that gives the target FDR, will run through maxCycles and return closest threshold if targetFDR is not reached.

findStartStopThresholds

public double[] findStartStopThresholds(double startThreshold,
                                        double stopThreshold)

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

printDocs

public static void printDocs()