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.