extractCTDC: CTD Descriptors - Composition

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

View source: R/desc-07-CTDC.R

Description

This function calculates the Composition descriptor of the CTD descriptors (dim: 21).

Usage

1

Arguments

x

A character vector, as the input protein sequence.

Value

A length 21 named vector

Note

For this descriptor type, users need to intelligently evaluate the underlying details of the descriptors provided, instead of using this function with their data blindly. It would be wise to use some negative and positive control comparisons where relevant to help guide interpretation of the results.

Author(s)

Nan Xiao <https://nanx.me>

References

Inna Dubchak, Ilya Muchink, Stephen R. Holbrook and Sung-Hou Kim. Prediction of protein folding class using global description of amino acid sequence. Proceedings of the National Academy of Sciences. USA, 1995, 92, 8700-8704.

Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim. Recognition of a Protein Fold in the Context of the SCOP classification. Proteins: Structure, Function and Genetics, 1999, 35, 401-407.

See Also

See extractCTDT and extractCTDD for Transition and Distribution of the CTD descriptors.

Examples

1
2
x = readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractCTDC(x)

Example output

 hydrophobicity.Group1  hydrophobicity.Group2  hydrophobicity.Group3 
            0.29715302             0.40569395             0.29715302 
normwaalsvolume.Group1 normwaalsvolume.Group2 normwaalsvolume.Group3 
            0.45195730             0.29715302             0.25088968 
       polarity.Group1        polarity.Group2        polarity.Group3 
            0.33985765             0.33274021             0.32740214 
 polarizability.Group1  polarizability.Group2  polarizability.Group3 
            0.33096085             0.41814947             0.25088968 
         charge.Group1          charge.Group2          charge.Group3 
            0.11032028             0.79003559             0.09964413 
secondarystruct.Group1 secondarystruct.Group2 secondarystruct.Group3 
            0.38967972             0.29537367             0.31494662 
  solventaccess.Group1   solventaccess.Group2   solventaccess.Group3 
            0.43060498             0.29715302             0.27224199 

protr documentation built on July 15, 2018, 9:05 a.m.