trans.misc
Class ConvertGeoData

java.lang.Object
  trans.misc.ConvertGeoData

public class ConvertGeoData

extends java.lang.Object

Reads and parses in a GEO data file into a tpmap and xxx.cela files for TiMAT2 processing. ie #ID_REF = #Rval = Cy5 (red) signal, Input total DNA from WI38 cells #Gval = Cy3 (green) signal, MeDIP DNA from WI38 cells #VALUE = log2(Gval/Rval) ID_REF Rval Gval VALUE CHR1P000009757_HSAP0406S00000003 2934.44 6303.33 1.1030 CHR1P000009637_HSAP0406S00000003 4742.78 13346.00 1.4926 CHR1P000009627_HSAP0406S00000003 3311.56 8825.89 1.4142 CHR1P000009617_HSAP0406S00000003 3295.78 8769.11 1.4118 CHR1P000009607_HSAP0406S00000003 3812.56 10092.00 1.4044 Saves xxx.cela files, and a xxx.tpmap

Constructor Summary

ConvertGeoData(java.lang.String[] args)

Method Summary

int	countDataLines(java.io.File file)
static void	main(java.lang.String[] args)
boolean	parseIt(java.io.File file)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ConvertGeoData

public ConvertGeoData(java.lang.String[] args)

Method Detail

parseIt

public boolean parseIt(java.io.File file)

countDataLines

public int countDataLines(java.io.File file)

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

printDocs

public static void printDocs()

main

public static void main(java.lang.String[] args)