Package trans.anno

For associating intervals, binding regions, and binding peaks with GFF annotation.

See:
Description

Class Summary

AnnotateRegions	For annotating Intervals or binding regions with gene information, proximity, neighbors, and bias based on random trials.
AnnotateRegionsWithGeneList	For annotating a picks file (chr, start, stop) with gene information for a particular list of CG names.
BindingRegion	For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.
BindingRegionComparator
BindingRegionsToGff3	Converts a Binding GenomicRegion file into GFF3 format.
BindingRegionsToIntervals	Converts binding regions to intervals setting the binding region as the best window and adds 2kb on either side.
DmelCGNameCoordinatePrinter	Prints genome coordinates for Dmel Rel 4 GFF3 CG names.
Gff2ToBindingRegions	Converts a gff2 file to a binding region file (chr start end mockSequence).
Gff2ToIntervals	Converts a gff2 file to an interval object file.
IntersectBindingPeaks	Performs an intersection analysis on two peak pick files (chr peakPosition score).
IntersectKeyWithRegions	Takes a key from a spike in experiment and sorted lists of regions to calculate TPR, FPR, and FDR for every threshold
IntersectRegions	Performs an intersection analysis on binding region files (chr start stop (optional fraction gc)).
MergeRegions	Takes several tab delimited region files (chrom, start, stop, ...), creates the union and writes to disk.
RandomRegions	Use to generate random regions of a defined length from a file of regions (chrom, start, stop).
Region	Represents a genomic region.
RegionComparator

Package trans.anno Description

For associating intervals, binding regions, and binding peaks with GFF annotation.