Package trans.tpmap

For maping, filtering, and calculating statistics about text version bpmap files.

See:
Description

Class Summary

BlastFilterResult	Container for a blast result: chromosome, numMatches, exactMatches, oneBPMismatches, startExactMatch.
CollapseTPMap	Collapses a text version bpmap into a unique set of bpmap lines base on the oligo sequence.
ConvertTPMapsToFeatures	Converts TPMaps to MapFeature[] and saves them to disk.
FilterTPMapByRegions	Filters a TPMap file by regions (tab delimited: chr start stop).
IntensityFeature	Minimal info about a feature for combining multiple chips together.
MapFeature	Tpmap line broken into some components, chromosome, start, pmX, pmY, and optionally, mmX, mmY.
MapSplitter	Splits a '.bpmap' text file into different chromosomes, helper script for TPMapProcessor.
MummerMapper	Application to map 1lq files to fasta files.
OligoFlipper	This reversed the oligo sequence and orientation in a tpmap file.
Stat1lq
StatTPMap	Calculates simple stats on a tpmap file, number unique oligos, number of lines, gc, tm...
StatTPMapControlSeqs
TPMapDensityReducer	Randomly drops a certain fraction of tpmap lines.
TPMapDuplicateFilter	For extracting duplicate oligo/ features from Affy's bpmap file, can be used as a stand alone but better to use TPMapProcessor.
TPMapFeature	Container for info about a particular oligo feature from a tpmap file.
TPMapLine	Minimal tpmap line, chrom, start, nothing else.
TPMapOligoBlastFilter	Application for remapping and filtering a text version bpmap file with BLAST.
TPMapProcessor	App for processing the tpmap file for use by downstream TiMAT applications.
TPMapSort	This sorts a tpmap first by chromosome, second by base position.
TPMapStripHighLowGC	Strips a tpmap file of lines where the %GC is > 0.6 or < 0.4.
WindowMaker	Creates Windows (start position, end position) of a given length, containing a given number of oligo start positions and maximum number of features.

Package trans.tpmap Description

For maping, filtering, and calculating statistics about text version bpmap files. Use the ProbeExporter application from Affy to convert your binary bpmap to a text version.