POpCan 0.7.2

Percentage Overlap Tool

POpCan

Tool for analysing the extent of overlap between various cancers including user-defined sub categories.

Input File Pre-requisites

• The input file should be a .csv file with "specific" column headers as a combination of 3 words separated by the character "_".
• 1 word for the main category and 2 words for subsequent sub-categories.
• The absence of sub-categories is accounted for in the calculations. Hence, if there are no sub-categories that the user wishes to specify, this can be replaced with a space between the character "_"

Column Header Example

• Main-category: A 4-letter acronym (such as 'STAD' for Stomach Adenocarcinoma). The length of the 4-letter acronym cannot be changed, but, it can be replaced with an equivalent 4-letter acronym as per user requirement for any other cancer type or disease type.
• First subcategory: Can be stage or a different user-defined variable (Ex. STAD_StageI).
• Second subcategory: Can be gene expression pattern or a different user-defined variable (Ex. STAD_StageI_Downregulated).
• If sub-categories were to be absent in the above example; STAD_StageI_Downregulated would be replaced with STAD_[Empty space]_[Empty space]

Available Parameters

• Input_Path : [string] path to the input file
• Condition : [string] either 'Between' or 'Within'. Between will find overlap only between two or more cancer types / disease conditions including their sub-categories but not for sub-categories within the same cancer type / disease condition. Within will compare the overlap between the sub-categories of same cancer type / disease condition as well.
• Output_Path : [string] path to the output file

Output Files

• Reports the extent of overlap as a percentage, the number of entries that overlap and the entries that overlap.

Installation

pip install POpCan

Use Case

#=============================Example===========================#
from POpCan import load_example_data_path, get_output_path, Find_Overlap
example_data = load_example_data_path()         #Input Path to Example File
example_output = get_output_path()              #Output Path to Example Output, Saves the output into Downloads directory


#Find_Overlap(Path_to_InputFile, "Between", Path_to_OutputFile)
Find_Overlap(example_data, "Between", example_output)

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CONTACT INFORMATION

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