calculateF: Calculate F1 or F2 Descriptors

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Calculate F1 or F2 Descriptors

Description

This function calculates F1 or F2 descriptors:

• F1 - sum of squared length of Single Amino Acid Repeats (SARs) in the entire protein sequence.

• F2 - maximum of the sum of Single Amino Acid Repeats (SARs) in a window of 6 residues.

Usage

calculateF(x, type = c("F1", "F2"))

Arguments

x	A data.frame containing gene/protein names and their fasta sequences.
type	The descriptor type: F1 or F2.

Details

calculateF

Value

A length 20 named vector for the data input.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

References

Alguwaizani, S., Park, B., Zhou, X., Huang, D.-S., and Han, K. (2018). Predicting interactions between virus and host proteins using repeat patterns and composition of amino acids. J. Healthc. Eng. 2018.

Examples

data(UP000464024_df)
x_df <- calculateF(UP000464024_df, type = "F1")
head(x_df, n = 2L)

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