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

autoCorrelation {Peptides} | R Documentation

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

### Description

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

### Usage

    autoCorrelation(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 shortest peptide minus one.
`property` | A property to use as value to be correlated.
`center` | A logical value `TRUE` or `FALSE` if the property must be centered.

### Value

The computed auto-correlation 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-correlation index for a lag=1
    autoCorrelation(
      sequence = "SDKEVDEVDAALSDLEITLE",
      lag = 1,
      property = AAdata$Hydrophobicity$KyteDoolittle,
      center = TRUE
    )
    # [1] -0.3519908

    # Calculate the auto-correlation index for a lag=5
    autoCorrelation(
      sequence = "SDKEVDEVDAALSDLEITLE",
      lag = 5,
      property = AAdata$Hydrophobicity$KyteDoolittle,
      center = TRUE
    )
    # [1] 0.001133553

[Package Peptides version 2.4.4 Index]