Uses of Package
trans.main

Packages that use trans.main

trans.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
trans.graphics	For graphically representing '.cel' files and intervals.
trans.main	Principle classes and scripts used in TiMAT2 analysis.
trans.misc	Rough working scripts.

Classes in trans.main used by trans.anno

Interval
Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

Window
Class to hold information about a window, a defined portion of the genome typically < 1kb.

Classes in trans.main used by trans.graphics

Interval
Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

Oligo
Container to hold information about a particular oligo.

Classes in trans.main used by trans.main

BindingPeak
Holds information about a binding peak within an interval.

Interval
Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

Oligo
Container to hold information about a particular oligo.

PosRegion
For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.

SubWindow
Class to hold information about a subWindow.

WilcoxonSamplePair
Used by the WilcoxonSignedRankTest.

Window
Class to hold information about a window, a defined portion of the genome typically < 1kb.

Classes in trans.main used by trans.misc

Interval
Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

Window
Class to hold information about a window, a defined portion of the genome typically < 1kb.