Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/519-extractPCMMDSScales.R

Generalized Scales-Based Descriptors derived by Multidimensional Scaling

1 | ```
extrPCMMDSScales(x, propmat, k, lag, scale = TRUE, silent = TRUE)
``` |

`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
( |

`silent` |
Logical. Whether we print the |

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

A length `lag * p^2`

named vector,
`p`

is the number of scales (dimensionality) selected.

Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>

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 `extrPCMScales`

for generalized scales-based
descriptors derived by Principal Components Analysis.

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