calculateKSAAP: Calculate k-spaced Amino Acid Pairs (KSAAP) Descriptor

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Calculate k-spaced Amino Acid Pairs (KSAAP) Descriptor

Description

This function calculates k-spaced Amino Acid Pairs (KSAAP) Descriptor for data input. This function is adapted from the CkSAApair function in the ftrCOOL package.

Usage

calculateKSAAP(x, spc = 3)

Arguments

x	A data.frame containing gene/protein names and their fasta sequences.
spc	A number of spaces separating two adjacent residues by a distance of spc, which can be any number up to two less than the length of the peptide; default to 3.

Details

calculateKSAAP

Value

A length 400 named vector for the data input.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

References

Kao, H.-J., Nguyen, V.-N., Huang, K.-Y., Chang, W.-C., and Lee, T.-Y. (2020).SuccSite: incorporating amino acid composition and informative k-spaced amino acid pairs to identify protein succinylation sites. Genomics. Proteomics Bioinformatics 18, 208–219.

Examples

data(UP000464024_df)
x_df <- calculateKSAAP(UP000464024_df)
head(x_df, n = 2L)

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.