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

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

Description

Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support

Usage

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

Arguments

x	A character vector, as the input protein sequence. Use '-' to represent gaps in the 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 amino acid properties based scales descriptors (protein fingerprint) with gap support. 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>

Examples

# amino acid sequence with gaps
x = readFASTA(system.file('protseq/align.fasta', package = 'BioMedR'))$`IXI_235`
fp = extrProtFPGap(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)

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