trans.misc
Class ConvertAgilentData
java.lang.Object
trans.misc.ConvertAgilentData
- public class ConvertAgilentData
- extends java.lang.Object
Reads in an Agilent tiling data file and outputs a tpmap and four cela files.
Cela files only contain intensities for chromosome mapped oligos, control intensities are set to zero.
Agilent uses zero based inter digit numbering, just like UCSC.
Assumes each oligo is a 60mer.
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ConvertAgilentData
public ConvertAgilentData(java.lang.String[] args)
parseAgilentFile
public boolean parseAgilentFile()
writeCelaFiles
public void writeCelaFiles()
writeSgrFiles
public boolean writeSgrFiles()
saveTPMap
public boolean saveTPMap()
save1lq
public boolean save1lq()
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)