Package trans.roc

For manipulating the BAC dmel spike in data and generating ROC curves.

See:
Description

Class Summary

Bin	Score collector for Sgr apps.
ControlGene
ExonScoreExtractor	Extracts scores from xxx.bar files for particular groups of exons.
ExtractNonOverlappingWindows	Parses out non overlapping RocWindows.
ExtractSaveSgrScores	Application for extracting and saving the scores from a .sgr file as a serialized float[].
ExtractScoresForRoc	Assignes values from an sgr file to a collection of RocWindows.
Gr	Gr line container.
GrComparator
MethodTester	Application for scoring '.sgr' files for positives and negatives in relation to known (spike in) data.
ParseBarsForParticularRegions	Returns oligo values that overlap particular regions.
ParsePatternedWindows	Finds RocWindows upstream and withing the neighborhood of the ATG start site of a patterned gene list.
ParseSgrsForParticularRegions	Returns oligo values that overlap particular regions.
ParseSgrsForParticularScores	Returns oligo values that overlap particular regions.
Positive	Container for a positive BAC used by the Sgr scripts.
PositiveComparator
PWMScoreWindows	Scores windows for hits to a transcription factor PWM, for RocWindow filtering.
RocWindow	For holding information about a region for ROC analysis.
RocWindowScanner	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.
Sgr	Sgr line container.
SgrBacCounter	Application for scoring '.sgr' files for positives and negatives in relation to the BAC spike in data.

Package trans.roc Description

For manipulating the BAC dmel spike in data and generating ROC curves.