Package trans.main

Principle classes and scripts used in TiMAT2 analysis.

See:
Description

Class Summary

BindingPeak	Holds information about a binding peak within an interval.
BindingRegionGraphPrinter	For printing chromosome specific .sgr files from IntervalPloter .txt picks files.
ChromSet
ExportIntervalData
FDRVsQValues
FDRWindowConverter	Associates an empirical FDR estimate with each window provided a mock IP was performed.
FindSubBindingRegions	Finds the best sub window and binding peaks (using the PeakPicker) within each interval.
IntensityPrinter	Prints out processed '.celp' files as '.sgr' files for import into Affy's IGB.
Interval	Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....
IntervalComparator	Class to help sort an array of Interval[] by chromosome, start position, length shortest first.
IntervalFilter	Sorts an Interval[] into two groups, those that pass or fail a variety of filters.
IntervalGFFPrinter	Prints intervals as a GFF3 File.
IntervalGraphPrinter	Prints an array of Interval as an '.sgr' file for import into IGB.
IntervalMaker	Collapses an array of Window into and array of Interval based on scores.
IntervalReportPrinter	Prints all things contained within an interval to a spreadsheet or a report card.
LoadChipSetIntervalOligoInfo	Loads arrays of Interval[] with oligo and sequence information needed for other applications.
LoadIntervalOligoInfo	Loads arrays of Interval[] with oligo and sequence information needed for other applications.
MakeAllWindows	Makes all windows given oligo positions.
MergeWindowArrays
MultiSGRPrinter	Prints a multi sgr file (chr position val1, val2, val3, ....)
MultiWindowIntervalMaker	Collapses arrays of Windows into an array of Interval based on scores and minimal number of windows that must pass.
Oligo	Container to hold information about a particular oligo.
OligoIntensityPrinter	Prints out the oligo intensity values, split by chromosome, as '.sgr' files for import into Affy's IGB.
OverlapCounter	Provides an intersection analysis on multiple Interval[]s.
OverlappingWindowScoreExtractor	Finds the best overlapping Window for each region and prints that score with the region information.
PeakPicker	Finds peaks in Intervals, both flat topped or peaks with sloping sides.
PosRegion	For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.
RandomizeLabels
ReplaceWindowScores
SamChromosomeData
ScanChip	Scores windows of intensity values using several tests.
ScanChromosomes	Scores windows of intensity values using several tests.
ScanGenes	Given a list of genes and their exons extracts the associated intensities.
ScoredGene
ScoreIntervals	Scores Intervals for the presence of transcription factor binding sites.
SetNumberIntervalMaker	Determines the threshold(s) needed to generate a set number of intervals, multiple score indexes accepted.
SplitWindowArraysByChromosome
SubWindow	Class to hold information about a subWindow.
T2	Runs entire TiMAT2 suite based on a parameter file.
T2Parameter	Container with info related to runing multiple T2 programs.
TestScanChip	Scores windows of intensity values using several tests.
WilcoxonRankSumTest	Implementation of a Wilcoxon Rank Sum Test.
WilcoxonSample	Used by the WilcoxonRankSumTest.
WilcoxonSamplePair	Used by the WilcoxonSignedRankTest.
WilcoxonSignedRankTest	Implementation of a Wilcoxon Signed Rank Test.
Window	Class to hold information about a window, a defined portion of the genome typically < 1kb.
WindowBlockMaker	Converts a Window[] into a heat map specific sgr file for import into IGB.
WindowBlockMakerTwoColor	Converts a Window[] into a heat map specific bar file for import into IGB.
WindowComparator	Class to help sort an array of Window[] by chromosome, start position, length shortest first.

Package trans.main Description

Principle classes and scripts used in TiMAT2 analysis.