extractPCMPropScales {Rcpi} | R Documentation

## Generalized AA-Properties Based Scales Descriptors

### Description

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`.

### 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)

Nan Xiao <https://nanx.me>

### 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)

[Package Rcpi version 1.20.1 Index]