categorize_nterm: Categorize and count N-terminal peptides based on Uniprot...

In MiguelCos/fragNterminomics: Annotation and processing of peptides from FragPipe search results

Categorize and count N-terminal peptides based on Uniprot processing annotation

Description

Categorize and count N-terminal peptides based on Uniprot processing annotation

Usage

categorize_nterm(annotated_peptides, uniprot_features, distinct = TRUE)

Arguments

annotated_peptides	data frame of annotated peptides. The output of the 'annotate_nterm' function.
uniprot_features	a list of data frames. Each data frame containing Uniprot-annotated features of proteins identified with N-terminal peptides, as resulting from the 'feature_to_dataframe' function of the 'drawProteins' package.
nterm	a character vector. Defines the type of modification expected to be found in N-terminal peptides. 'c("TMT-labelled", "acetylated")' is default.

Value

a list with 4 elements: 'ntermini_n_processing_features': data frame of N-terminally identified proteins and their annotated processing features. 'ntermini_category': data frame of categorized N-terminal peptides according to their matching to annotated processing sites. 'ntermini_category_counts': data frame of counts of matched features and locations to annotated processing sites. 'ntermini_category_plot': ggplot2 object. Visualization of counts of matched features and locations.

MiguelCos/fragNterminomics documentation built on Oct. 13, 2023, 5:31 a.m.