calculateKSAAP {HPiP} | R Documentation

## 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, matinerb.94@gmail.com

### 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)

[Package HPiP version 1.0.0 Index]