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Calculation methods
The three folders below each represent a section. Each file in these folders represents a step. In a file there is a function for each method.
This folder contains the methods used for importing mass spectrometry data and metadata. Its methods always have the following signature: an input dataframe and any other method parameters. They return a protein intensities dataframe and a dict of other outputs.
This folder contains the methods for filtering, imputation, normalisation, outlier detection and methods to create the corresponding plots. Its methods have the same signature as importing, receiving an input dataframe plus the method's parameters and returning a transformed dataframe together with a dict that contains other outputs specific to the method, such as dropouts, p-values or other values. The dataframe that is used as input is the output of the previous importing/data preprocessing step.
This folder contains methods that are used to analyse the outputs of the data preprocessing section and previous data analysis steps. Always using the previous output dataframe as input gets replaced by naming the steps that should be used and choosing the right named step as input. On this section the calculation and the plots be can separated from each other. In the case of the calculation methods, they return a dictionary including dataframes and other outputs. On the other hand, plot methods return a list of figures.