PythonCalculation

Python code for calculation

GiniCorrelationCoefficient.py

Calculate Gini Correlation Coefficient (GCC). This is one sped up version in Python of GCC from rsgcc Package
(https://cran.r-project.org/web/packages/rsgcc/index.html). The running speed is improved by

1. parallelization. and 2) pre-calculation of some statics per gene to avoid repetitive calculation in loops.

numpy, multipleprocessing, pandas modules are imported in this code.

usage:

module load python/2.7.8
python GiniCorrelationCoefficient.py    matrix   output    threadnum  

matrix : input matrix file with headline(sample IDs) and row names(gene IDs), each row contains data for each gene.
output: output file
threadnum: number of cores to be used