pat.transformation

Class AFS

java.lang.Object

pat.transformation.AFS

public class AFS
extends java.lang.Object

Transform gene expression level by AFS method

Constructor Summary

Constructors

Constructor and Description
AFS(java.lang.String dataFile, java.lang.String labelFile, java.lang.String annotationFile, java.lang.String pcogFile) Constructor requires dataFile = series_matrix gene expression data labelFile = labels of the subject in tab delimited format annotationFile = annotation file of microarray platform (GPLXXX) pcogFile = file contains PCOGs of each pathway/gene set

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String[]	getAllParameters() Get all parameter as String[]
void	printDetail() Print parameter values
java.util.ArrayList<java.util.ArrayList>	transformTesting() Transform gene expression level to pathway activity by using PCOGs set of Training data
java.util.ArrayList<java.util.ArrayList>	transformTraining(java.lang.String pathwayFile) Transform gene expression level to pathway activity by identifying PCOGs set pathwayFile = file contain pathway/gene set members

Methods inherited from class java.lang.Object

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

Constructor Detail

AFS

public AFS(java.lang.String dataFile,
   java.lang.String labelFile,
   java.lang.String annotationFile,
   java.lang.String pcogFile)

Constructor requires dataFile = series_matrix gene expression data
labelFile = labels of the subject in tab delimited format
annotationFile = annotation file of microarray platform (GPLXXX)
pcogFile = file contains PCOGs of each pathway/gene set

Method Detail

transformTraining

public java.util.ArrayList<java.util.ArrayList> transformTraining(java.lang.String pathwayFile)
                                                           throws java.lang.Exception

Transform gene expression level to pathway activity by identifying PCOGs set
pathwayFile = file contain pathway/gene set members

Throws:

java.lang.Exception

transformTesting

public java.util.ArrayList<java.util.ArrayList> transformTesting()
                                                          throws java.lang.Exception

Transform gene expression level to pathway activity by using PCOGs set of Training data

Throws:

java.lang.Exception

printDetail

public void printDetail()

Print parameter values

getAllParameters

public java.lang.String[] getAllParameters()

Get all parameter as String[]