extractPCMDescScales {Rcpi} | R Documentation

## Scales-Based Descriptors with 20+ classes of Molecular Descriptors

### Description

Scales-Based Descriptors with 20+ classes of Molecular Descriptors

### Usage

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

### Arguments

`x` | A character vector, as the input protein sequence.
`propmat` | The matrix containing the descriptor set for the amino acids, which could be chosen from `AAMOE2D`, `AAMOE3D`, `AACPSA`, `AADescAll`, `AA2DACOR`, `AA3DMoRSE`, `AAACF`, `AABurden`, `AAConn`, `AAConst`, `AAEdgeAdj`, `AAEigIdx`, `AAFGC`, `AAGeom`, `AAGETAWAY`, `AAInfo`, `AAMolProp`, `AARandic`, `AARDF`, `AATopo`, `AATopoChg`, `AAWalk`, `AAWHIM`.
`index` | Integer vector or character vector. Specify which molecular descriptors to select from one of these deseriptor sets by specify the numerical or character index of the molecular descriptors in the descriptor set. Default is `NULL`, means selecting all the molecular descriptors in this descriptor set.
`pc` | Integer. The maximum dimension of the space which the data are to be represented in. 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 (`propmat`) before doing MDS? 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 scales-based descriptors with molecular descriptors sets calculated by Dragon, Discovery Studio and MOE. Users could specify which molecular descriptors to select from one of these deseriptor sets by specify the numerical or character index of the molecular descriptors in the descriptor set.

### Value

A length `lag * p^2` named vector, `p` is the number of scales selected.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

See `extractPCMScales` for generalized AA-descriptor based scales descriptors.

### Examples

    x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
    descscales = extractPCMDescScales(x, propmat = 'AATopo', index = c(37:41, 43:47),
                                      pc = 5, lag = 7, silent = FALSE)

[Package Rcpi version 1.20.1 Index]