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#Usage:

#####reducer.py: used to find all common tumors between transposed expression and CNA data and writes the common tumors to OutputFile.

python reducer.py [EXPRESSIONS (IlluminaHiSeq)] [CNA] [OutputFile]

#####transpose.py: takes in a matrix file where the rows are genes and the columns are tumors and transposes the file

python transpose.py [InputMatrix] [OutputMatrix]

#####annotation.py: takes in the tissueSourceSite.txt and CommonTumors outputted by reducer.py and outputs a file with cancer names and their corresponding TCGA tumor IDs

python annotation.py [CommonTumors]

#####cdfMaker.py: takes in two transposed matrix files: NormalMatrix and a TumorMatrix, and outputs OutputFile, which is a matrix of the CDFs for each element

python cdfMaker.py [NormalMatrix] [TumorMatrix] [OutputFile]

#####cnaExpExtractor.py: takes in three files, two transposed matrix files: CNA matrix and Expression Matrix, and one common tumor list, and outputs two files that are the common tumors between the CNA and Expression matrices

python cnaExpExtractor.py [CNA] [EXPRESSIONS] [CommonTumors] [OutputCNA] [OutputExpression]

#####normalFinder.py: takes in one transposed Expression matrix and outputs a matrix of normal samples

python normalFinder.py [EXPRESSIONS] [OutputNormalMatrix]

All code written by Ritwik Gupta and Kevin Lu under the lab of Dr. Xinghua Lu at the Department of Biomedical Informatics, University of Pittsburgh.