Use this Package for easiest way to handle the data for GPTwoSample.
This Module is for easy access to data structures gptwosample works with.
Created on Mar 18, 2011
@author: Max Zwiessele
Bases: exceptions.TypeError
Thrown, if DataStructure given does not fit. Training data training_data has following structure:
{input_id : {'group 1':[double] ... 'group n':[double]},
output_id : {'group 1':[double] ... 'group n':[double]}}
Returns the valid structure for model dictionaries, used in gptwosample. Make sure to use this method if you want to use the model structure in this package!
For convienent usage this module provides IO operations for data
Created on Jun 9, 2011
@author: Max Zwiessele, Oliver Stegle
Return data from csv file with delimiter delimiter in form of a dictionary. Missing Values are all values x which cannot be converted float(x)
The file format has to fullfill following formation:
arbitrary | x1 | ... | xl |
---|---|---|---|
Gene Name 1 | y1 replicate 1 | ... | yl replicate 1 |
... | ... | ... | ... |
Gene Name 1 | y1 replicate k1 | ... | yl replicate k1 |
... | |||
Gene Name n | y1 replicate 1 | ... | yl replicate 1 |
... | ... | ... | ... |
Gene Name n | y1 replicate kn | ... | yl replicate kn |
Returns: {“input”:[x1,...,xl], “Gene Name 1”:[[y1 replicate 1, ... yl replicate 1], ... ,[y1 replicate k, ..., yl replikate k]]}
Write given data in training_data_structure (see gptwosample.data.data_base for details) into file for path_to_file.
Parameters: