R: Compute the auto-covariance index of a protein sequence

autoCovariance {Peptides} | R Documentation

## Compute the auto-covariance index of a protein sequence

### Description

This function computes the Cruciani et al (2004) auto-corvariance index. The `autoCovariance` index is calculated for a lag 'd' using a descriptor 'f' (centred) over a sequence of length 'L'.

### Usage

    autoCovariance(sequence, lag, property, center = TRUE)

### Arguments

`sequence` | An amino-acids sequence
`lag` | A value for a lag, the max value is equal to the length of the shortest peptide minus one.
`property` | A property to use as value to evaluate the covariance.
`center` | A logical value `TRUE` or `FALSE` if the property must be centered.

### Value

The computed auto-covariance index for a given amino-acids sequence

### References

Cruciani, G., Baroni, M., Carosati, E., Clementi, M., Valigi, R., and Clementi, S. (2004) Peptide studies by means of principal properties of amino acids derived from MIF descriptors. J. Chemom. 18, 146-155.

### Examples

    # Loading a property to evaluate its autocorrelation
    data(AAdata)

    # Calculate the auto-covariance index for a lag=1
    autoCovariance(
      sequence = "SDKEVDEVDAALSDLEITLE",
      lag = 1,
      property = AAdata$Hydrophobicity$KyteDoolittle,
      center = TRUE
    )
    # [1] -0.4140053

    # Calculate the auto-covariance index for a lag=5
    autoCovariance(
      sequence = "SDKEVDEVDAALSDLEITLE",
      lag = 5,
      property = AAdata$Hydrophobicity$KyteDoolittle,
      center = TRUE
    )
    # [1] 0.001000336

[Package Peptides version 2.4.4 Index]