Enrichment

alpaca.gathers(df, enrichment_standards, preparation, lfq_method='iBAQ', plot=False, save_plot=False)

Calculates enrichment factors for protein standards spiked into samples and optionally plots the results.

Parameters:

• df (pandas.DataFrame):
  DataFrame containing the quantified protein data (e.g., with iBAQ or LFQ values).

• enrichment_standards (pandas.DataFrame or file-like object):
  DataFrame or file containing the standard information for calculating enrichment.

• preparation (pandas.DataFrame):
  DataFrame containing information about the experimental preparation (e.g., conditions).

• lfq_method (str, optional, default='iBAQ'):
  Label-free quantification method used in the analysis (e.g., 'iBAQ', 'LFQ').

• plot (bool, optional, default=False):
  Whether to plot the enrichment factors.

• save_plot (bool, optional, default=False):
  Whether to save the plot as a file.

Returns:

• e_test (pandas.DataFrame):
  DataFrame containing calculated enrichment values for each sample.

• preparation (pandas.DataFrame):
  Updated preparation DataFrame with enrichment factors added.

Notes:

• The function calculates the enrichment factors by comparing the protein levels in the experimental samples to the spiked-in standards.
• It groups the data by experimental conditions and replicates to calculate median enrichment values.
• The function also optionally generates and saves a plot of the enrichment values.