/igp

In group proportion to assess generalisability of clustering tendency

igp_script_reduced.r

R script computing in-group proportions [PMID: 16613834] and associated p-values between cluster prototypes (training_data_reduced.Rds) and testing data.

Dependencies

parallel 3.6.0.

Input files

Normalised expression values as a CSV file:

  • header: HGNC gene identifiers
  • index: sample/patient identifiers

Output files

Rds file (rna_data_reduced_clusterRepro.Rds) containing in-group proportion values and p-values.

Arguments

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.

Example

From a terminal window, navigate to the igp_folder_reduced_parallel and run Rscript igp_script_reduced.r test_data.csv num_cores