calc_features: Calculate statistical and physicochemical features for...

In fcampelo/epitopes: Processing and Feature Extraction for Epitope Data

Calculate statistical and physicochemical features for peptides

Description

This function is used to calculate several distinct families of features for a vector of peptides.

Usage

calc_features(df, max.N = 2, ncpus = 1, save_folder = NULL)

Arguments

df	a data.table of class windowed_epit_dt or windowed_prot_dt, generated by make_window_df()
max.N	maximum length of N-peptide frequency features to be calculated.
ncpus	number of cores to use.
save_folder	path to folder for saving the output.

Details

This function is partially based on functions Peptides::aaComp() and Peptides::aaDescriptors() (check documentation for details).

Some of the features are calculated based on an aminoacid propensity scale, which was originally obtained from E.L. Ulrich et al., "BioMagResBank". Nucleic Acids Research 36, D402-D408 (2008) DOI: 10.1093/nar/gkm957. The data was downloaded from http://www.bmrb.wisc.edu/ref_info/aadata.dat on July 1, 2020.

Value

Data table containing the calculated features appended as new columns.

Author(s)

Felipe Campelo ([e-mail]); Jodie Ashford ([e-mail])

fcampelo/epitopes documentation built on April 22, 2023, 12:23 a.m.