Generalized AA-Properties Based Scales Descriptors

Generalized AA-Properties Based Scales Descriptors

Usage

extractPCMPropScales(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.

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.

See also

See extractPCMScales for generalized scales-based descriptors.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
propscales = extractPCMPropScales(x, index = c(160:165, 258:296), pc = 5, lag = 7, silent = FALSE)
#> Summary of the first 5 principal components:
#>                            PC1      PC2     PC3      PC4      PC5
#> Standard deviation     4.51689 2.786022 2.27000 1.757295 1.419412
#> Proportion of Variance 0.45338 0.172490 0.11451 0.068620 0.044770
#> Cumulative Proportion  0.45338 0.625870 0.74038 0.809000 0.853780