scripts package

Submodules

scripts.edgepy module

class scripts.edgepy.EdgePy(args)[source]

Bases: object

generate_results(gene_details: Dict[collections.abc.Hashable, Dict[collections.abc.Hashable, Any]], gene_likelihood1: Dict[collections.abc.Hashable, float], group_type1: str, group_type2: str) → List[str][source]

This function simply prepares a summary of the results of the analysis for dumping to file or to screen

Parameters:
  • gene_details – information about the genes - should contain fields ‘mean1’ and ‘mean2’ for display
  • gene_likelihood1 – dictionary of gene names and the p-value associated. used to sort the data
  • group_type1 – the name of the first grouping
  • group_type2 – the name of the second grouping
ks_2_samples()[source]

Run a 2-tailed Kolmogorov-Smirnov test on the DGEList object.

Parameters:None.
Returns:a dictionary of dictionary (key, gene), holding mean1 and mean2 for the two groups gene_likelihood: a dictionary (key, gene), holding the p-value of the separation of the two groups group_types: list of the groups in order.
Return type:gene_details
run_ks()[source]

First pass implementation of a Kolmogorov-Smirnov test for different groups, using the Scipy KS test two-tailed implementation.

Parameters:None.
scripts.edgepy.main()[source]
scripts.edgepy.parse_arguments(parser=None)[source]

Module contents