proteometer.lip_analysis#

Functions#

lip_analysis(→ tuple[pandas.DataFrame, ...)

Performs statistical analysis on the provided limited proteolysis data.

lip_pept_statistics(→ pandas.DataFrame)

lip_site_statistics(→ pandas.DataFrame)

Converts the double-peptide data frame to a site-level data frame.

Module Contents#

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

Performs statistical analysis on the provided limited proteolysis data.

Parameters:

  • par (Params) – Parameters for the limited proteolysis analysis, including file paths and settings.

  • drop_samples (list[str], optional) – List of samples to drop from the analysis. Defaults to None.

Returns:

The resulting limited

proteolysis data frames after analysis. These are the double-digested peptide data frame, the rollup of the peptide data to the single site, and the processed global protein data frame (in that order).

Return type:

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

proteometer.lip_analysis.lip_pept_statistics(lip_pept: pandas.DataFrame, prot_seqs: list[proteometer.fasta.SeqRecord], anova_cols: list[str], pairwise_ttest_groups: collections.abc.Iterable[proteometer.stats.TTestGroup], metadata: pandas.DataFrame, par: proteometer.params.Params) → pandas.DataFrame[source]#
proteometer.lip_analysis.lip_site_statistics(lip_site: pandas.DataFrame, anova_cols: list[str], pairwise_ttest_groups: collections.abc.Iterable[proteometer.stats.TTestGroup], metadata: pandas.DataFrame, par: proteometer.params.Params) → pandas.DataFrame[source]#

Converts the double-peptide data frame to a site-level data frame.

Parameters:

  • lip_pept (pd.DataFrame) – The double-peptide data frame.

  • prot_seqs (list[fasta.SeqRecord]) – The list of protein sequences.

  • int_cols (Iterable[str]) – The names of columns to with intensity values.

  • anova_cols (list[str]) – The columns for ANOVA.

  • pairwise_ttest_groups (Iterable[stats.TTestGroup]) – The pairwise T-test groups.

  • metadata (pd.DataFrame) – The metadata data frame.

  • par (Params) – The parameters for limitied proteolysis analysis.

Returns:

A data frame with the site-level data.

Return type:

pd.DataFrame