| COUSCOus {COUSCOus} | R Documentation |
COUSCOus is a residue-residue contact detecting method.
COUSCOus(fasta.file, verbose = TRUE)
fasta.file |
Protein sequence alignment file name in FASTA format. |
verbose |
Print tracing information. The default value is TRUE. |
Contact prediction using shrinked covariance (COUSCOus). COUSCOus is a residue-residue contact detecting method approaching the contact inference using the glassofast implementation of Matyas and Sustik (2012, The University of Texas at Austin UTCS Technical Report 2012:1-3. TR-12-29.) that solves the L_1 regularised Gaussian maximum likelihood estimation of the inverse of a covariance matrix. Prior to the inverse covariance matrix estimation we utilise a covariance matrix shrinkage approach, the empirical Bayes covariance estimator, which has been shown by Haff (1980) <DOI:10.1214/aos/1176345010> to be the best estimator in a Bayesian framework, especially dominating estimators of the form aS, such as the smoothed covariance estimator applied in a related contact inference technique PSICOV.
A data frame with 3 columns (i, j, pCorr) containing all possible pairs of residues along with their COUSCOus correlation value.
Reda Rawi, Matyas A. Sustik, Ben Calderhead
Maintainer: Reda Rawi <rrawi@qf.org.qa>
# Alignment file
file.fasta <- system.file( "examples/1oaiA0.fa", package = "COUSCOus" )
# Run COUSCOus
df.predictions <- COUSCOus( file.fasta )