crossCovariance {Peptides}

Compute the cross-covariance index of a protein sequence

Description

This function computes the Cruciani et al (2004) cross-covariance index. The lagged crossCovariance index is calculated for a lag 'd' using two descriptors 'f1' and 'f2' (centred) over a sequence of length 'L'.

Usage

crossCovariance(sequence, lag, property1, property2, 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.

property1

A property to use as value to evaluate the cross-covariance.

property2

A property to use as value to evaluate the cross-covariance.

center

A logical value TRUE or FALSE if the property must be centered.

Value

The computed cross-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 cross-covariance index for a lag=1
crossCovariance(
  sequence = "SDKEVDEVDAALSDLEITLE",
  lag = 1,
  property1 = AAdata$Hydrophobicity$KyteDoolittle,
  property2 = AAdata$Hydrophobicity$Eisenberg,
  center = TRUE
)
# [1] -0.3026609

# Calculate the cross-correlation index for a lag=5
crossCovariance(
  sequence = "SDKEVDEVDAALSDLEITLE",
  lag = 5,
  property1 = AAdata$Hydrophobicity$KyteDoolittle,
  property2 = AAdata$Hydrophobicity$Eisenberg,
  center = TRUE
)
# [1] 0.02598035