proteometer.ptm_analysis

Functions

ptm_analysis(→ tuple[pandas.DataFrame, pandas.DataFrame])	Runs the PTM proteomics processing and statistical analysis pipeline.
ptm_analysis_return_all(→ tuple[pandas.DataFrame, ...)	Runs the PTM proteomics processing and statistical analysis pipeline.

Module Contents

proteometer.ptm_analysis.ptm_analysis(par: proteometer.params.Params, drop_samples: list[str] | None = None) → tuple[pandas.DataFrame, pandas.DataFrame]

Runs the PTM proteomics processing and statistical analysis pipeline.

This function reads in data from proteomics files specified in the par object, and performs normalization and batch correction, site-level rollup, and statistical analysis. The resulting DataFrame contains the processed PTM data, including the statistical results.

Parameters:

• par (Params) – A Params object that contains all the parameters for the analysis.

• drop_samples (list[str], optional) – A list of samples to be dropped from the analysis. Default is None.

Returns:

Two pandas DataFrames that contains the result of the PTM analysis.

The first is the processed PTM data, and the second is the global proteomics data.

Return type:

tuple[pd.DataFrame,pd.DataFrame]

proteometer.ptm_analysis.ptm_analysis_return_all(par: proteometer.params.Params) → tuple[pandas.DataFrame, pandas.DataFrame, pandas.DataFrame]

Runs the PTM proteomics processing and statistical analysis pipeline.

This function reads in data from proteomics files specified in the par object, and performs normalization and batch correction, site-level rollup, and statistical analysis. The resulting DataFrame contains the processed PTM data, including the statistical results.

Parameters:

par – A Params object that contains all the parameters for the analysis.

Returns:

Three pandas DataFrames containing the results of the PTM analysis.

The first is the processed PTM data, which includes statistical results. The second is the global proteomics data, normalized and batch-corrected. The third is the uncorrected PTM data, which contains raw site-level data before normalization or correction.

Return type:

tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame]