R/kchem.R

In jpvert/kmr4toxicogenetics: Kernel multitask regression for toxicogenetics

#' Kernel matrices for chemicals
#' 
#' A list of example kernel matrices of chemical features.
#' 
#' @format A list of 32 kernel matrices for chemicals of five categories of cell line features:
#' \describe{
#'   \item{KcdkRbf}{10 kernel matrices of chemical descriptors calculated using the Chemistry Development Kit (CDK) provided by the challenge, corresponding to Gaussian RBF kernel with various bandwidth.}
#'   \item{Kchemcpp}{1 kernel matrix of a marginalized graph kernel, as implemented in the \code{ChemCPP} package, in the 2D structure of the chemicals.}
#'   \item{KpredtargetRbf}{10 kernel matrices based on the chemical descriptors by their predicted targets, corresponding to Gaussian RBF kernel with various bandwidth.}
#'   \item{KsirmsRbf}{10 kernel matrices of chemical descriptors generated by the Simplex representation of molecular structure (SIRMS) provided by the challenge, corresponding to Gaussian RBF kernel with various bandwidth.}
#'   \item{Ksubstructure}{1 kernel matrix (linear kernel) of the presence or absence of a list of predefined substructures from the PubChem fingerprint in the 2D structure of the chemicals.}
#' }
#' 
#' @references 
#' Bernard, E., Jiao, Y., Scornet, E., Stoven, V., Walter, T., and Vert, J.-P. (2017). "Kernel multitask regression for toxicogenetics." \href{https://doi.org/10.1101/171298}{bioRxiv-171298}.
#' 
#' @source \url{https://doi.org/10.7303/syn1761567}
#' 

"kchem"