extrPCMPropScales: Generalized AA-Properties Based Scales Descriptors

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description

Generalized AA-Properties Based Scales Descriptors

Usage

extrPCMPropScales(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.

Details

This function calculates the generalized amino acid properties based scales descriptors. Users could specify which AAindex properties to select from the AAindex database by specify the numerical or character index of the properties in the AAindex database.

Value

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

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

See Also

See extrPCMScales for generalized scales-based descriptors.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
propscales = extrPCMPropScales(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.