Package trans.misc

Rough working scripts.

See:
Description

Class Summary

AverageDoubles	Slides a 50 index window along an array averaging the contents.
Bar2Gr	Utility to convert simple one graph xxx.bar files to xxx.gr files.
Bed2Gr	Converts a bed file to multiple gr files.
CalcGCAndTransform	Parses out treatment and control oligo info from intervals, calculate GC and transform ratios based on GC corrector, see TransformRatios.
CalcGCRatiosFromIntervals	Parse out treatment and control oligo info from intervals, calculate GC and ratios to look for bias.
ConvertAgilentData	Reads in an Agilent tiling data file and outputs a tpmap and four cela files.
ConvertGeoData	Reads and parses in a GEO data file into a tpmap and xxx.cela files for TiMAT2 processing.
ConvertNimblegenNDF2TPMap	Converts a Nimblegen NDF txt file to a tpmap.!
ConvertNimblegenPAIR2Cela	Converts Nimblegen PAIR txt files to a cela files.!
CorrelateGrFiles
GCRatio	Container for a ratio and associated %GC content for a particular oligo.
Gr2Bar
GrGraph	Container for holding info related to a xxx.gr file.
InefficientPseudoMedian
PrependColumn
Regions2Intervals	Converts binding regions to intervals setting the binding region as the best window and adds 2kb on either side.
ScoredRegionsFormatFixer	Converts a file format to something usable by Excel from the joinRegionsWithScores.sh script.
Sgr2Bar
SgrComparator
TextPValOrSig2Gr	Converts a bed file to multiple gr files.
TransformRatios	Transforms ratio scores in Intervals based on the BAC GC Corrector.
Util	Static helper methods for all things Affy
WindowHistogram	Makes a histogram of scores from a Window[].

Package trans.misc Description

Rough working scripts.