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 |
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 2.4.6 Index]