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A

AFS - Class in pat.transformation

Transform gene expression level by AFS method

AFS(String, String, String, String) - Constructor for class pat.transformation.AFS

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

annotateArray(ArrayList<ArrayList>, String) - Static method in class pat.transformation.ReadAffy

anotherZTransform(ArrayList<ArrayList>) - Static method in class pat.transformation.ReadAffy

C

convert(ArrayList<ArrayList>, String, String) - Static method in class pat.classification.ToARFF

parameter
data = ArrayList matrix output = ARFF formated output file labels = list of possible labels separated by comma
.

CORG - Class in pat.transformation

Transform gene expression level by NCFSi method (Binary class only)

CORG(String, String, String, String) - Constructor for class pat.transformation.CORG

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

F

FileManager - Class in pat

FileManager() - Constructor for class pat.FileManager

G

getAllParameters() - Method in class pat.transformation.AFS

Get all parameter as String[]

getAllParameters() - Method in class pat.transformation.CORG

Get all parameter as String[]

getAllParameters() - Method in class pat.transformation.NCFSi

Get all parameter as String[]

N

NCFSi - Class in pat.transformation

Transform gene expression level by NCFSi method (Binary class only)

NCFSi(String, String, String, String) - Constructor for class pat.transformation.NCFSi

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

P

pat - package pat

pat.classification - package pat.classification

pat.transformation - package pat.transformation

printDetail() - Method in class pat.transformation.AFS

Print parameter values

printDetail() - Method in class pat.transformation.CORG

Print parameter values

printDetail() - Method in class pat.transformation.NCFSi

Print parameter values

R

ReadAffy - Class in pat.transformation

ReadAffy() - Constructor for class pat.transformation.ReadAffy

readArray(String) - Static method in class pat.transformation.ReadAffy

readCSV(String) - Static method in class pat.FileManager

readTab(String) - Static method in class pat.FileManager

removeQoute(ArrayList) - Static method in class pat.transformation.ReadAffy

T

ToARFF - Class in pat.classification

Convert ArrayList matrix to ARFF format for weka

ToARFF() - Constructor for class pat.classification.ToARFF

transformTesting() - Method in class pat.transformation.AFS

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

transformTesting() - Method in class pat.transformation.CORG

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

transformTesting() - Method in class pat.transformation.NCFSi

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

transformTraining(String) - Method in class pat.transformation.AFS

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

transformTraining(String) - Method in class pat.transformation.CORG

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

transformTraining(String) - Method in class pat.transformation.NCFSi

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

W

writeAttributes(Instances, String) - Static method in class pat.FileManager

writeCSV(ArrayList<ArrayList>, String) - Static method in class pat.FileManager

writeCSV(ArrayList<ArrayList>, String, ArrayList<Integer>) - Static method in class pat.FileManager

writeTab(ArrayList<ArrayList>, String) - Static method in class pat.FileManager

Z

zTransform(ArrayList<ArrayList>) - Static method in class pat.transformation.ReadAffy

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