R script computing in-group proportions [PMID: 16613834] and associated p-values between cluster prototypes (training_data_reduced.Rds) and testing data.
parallel 3.6.0.
Normalised expression values as a CSV file:
- header: HGNC gene identifiers
- index: sample/patient identifiers
Rds file (rna_data_reduced_clusterRepro.Rds) containing in-group proportion values and p-values.
The first argument corresponds to the testing data path and the second to the number of cores that will be used to run the permutations.
From a terminal window, navigate to the igp_folder_reduced_parallel and run Rscript igp_script_reduced.r test_data.csv num_cores