extractProtFP: Amino Acid Properties Based Scales Descriptors (Protein...

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)

Description

This function calculates amino acid properties based scales descriptors (protein fingerprint). Users can specify which AAindex properties to select from the AAindex database by specify the numerical or character index of the properties in the AAindex database.

Usage

extractProtFP(x, index = NULL, pc, lag, scale = TRUE, silent = TRUE)

Arguments

x	A character vector, as the input protein sequence.
index	Integer vector or character vector. Specify which AAindex properties to select from the AAindex database by specify the numerical or character index of the properties in the AAindex database. Default is NULL, means selecting all the AA properties in the AAindex database.
pc	Integer. Use the first pc principal components as the scales. Must be no greater than the number of AA properties provided.
lag	The lag parameter. Must be less than the amino acids.
scale	Logical. Should we auto-scale the property matrix before PCA? Default is TRUE.
silent	Logical. Whether we print the standard deviation, proportion of variance and the cumulative proportion of the selected principal components or not. Default is TRUE.

Value

A length lag * p^2 named vector, p is the number of scales (principal components) selected.

Author(s)

Nan Xiao <https://nanx.me>

Examples

x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
fp <- extractProtFP(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)

protr documentation built on Sept. 12, 2024, 6:44 a.m.