# Scales-Based Descriptors derived by Multidimensional Scaling

Source:`R/pcm-05-extractMDSScales.R`

`extractMDSScales.Rd`

This function calculates scales-based descriptors derived by Multidimensional Scaling (MDS). Users can provide customized amino acid property matrices.

## Arguments

- x
A character vector, as the input protein sequence.

- propmat
A matrix containing the properties for the amino acids. Each row represent one amino acid type, each column represents one property. Note that the one-letter row names must be provided for we need them to seek the properties for each AA type.

- k
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 to print the

`k`

eigenvalues computed during the scaling process or not. Default is`TRUE`

.

## References

Venkatarajan, M. S., & Braun, W. (2001). New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. Molecular modeling annual, 7(12), 445–453.

## See also

See `extractScales`

for scales-based
descriptors derived by Principal Components Analysis.

## Author

Nan Xiao <https://nanx.me>

## Examples

```
x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
data(AATopo)
tprops <- AATopo[, c(37:41, 43:47)] # select a set of topological descriptors
mds <- extractMDSScales(x, propmat = tprops, k = 5, lag = 7, silent = FALSE)
#> Eigenvalues computed during the scaling process:
#> [1] 1.266223e+02 5.846270e+01 4.058692e+00 6.994430e-01 1.529469e-01
#> [6] 3.434787e-03 4.284842e-04 4.918500e-05 3.626185e-06 3.042620e-10
#> [11] 2.295818e-15 1.850329e-15 1.455955e-15 1.208436e-15 6.929084e-16
#> [16] 5.639676e-16 -9.663800e-16 -1.207752e-15 -2.504939e-15 -3.313120e-15
```