MOHA algorithm published by John Graf and Maria Zavodszky, GE Global Research Center.
Please see the published paper for details.
First change the working directory to the location of the jar file that has a subdirectory called “example”. The next line computes thresholds from a cell stat file with the biomarker measures called quant_006.csv It will create the threshold filed called quant_006.csv.thresholds.txt
java -jar MOHAtool.jar -computeThresholds=example/quant_006.csv -biomarkerMetricTag=_Cell_Mean
Next you compute the cell states using the threshold file. It requires the inputted cell measures quant_006.csv and the threshold file that was generated in the previous step. The output of this step will be a couple files, one of them called “quant_006.csv.MarkerStates.txt” This will be used as input for the final step.
java -jar MOHAtool.jar -computeCellStates=example/quant_006.csv -thresholdFile=example/quant_006.csv.thresholds.txt
The final step is to compute the heterogeneity metrics You need to give it the input file “quant_006.csv.MarkerStates.txt” which will output the metrics to the file out_moha.txt.
java -jar MOHAtool.jar -computeHeterogeneity=example/quant_006.csv.MarkerStates.txt -outputFile=example/out_moha_006.txt -append=false
It would be preferable to have enough build files stored here that MOHAtool.jar can be easily rebuilt, rather than saving it in GitHub. (to-do)