Peptides (version 2.4.6)

autoCovariance: 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)

Value

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

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.

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