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.