Package trans.tpmap

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


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.
StatTPMap Calculates simple stats on a tpmap file, number unique oligos, number of lines, gc, tm...
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.