\name{runICA} \alias{runICA} \title{Run of fastICA and JADE algorithms} \usage{ runICA(method = c("fastICA", "JADE"), X, nbComp, alg.type = c("deflation", "parallel"), fun = c("logcosh", "exp"), maxit = 500, tol = 10^-6, ...) } \arguments{ \item{method}{The ICA method to use, either "JADE" (the default) or "fastICA".} \item{X}{A data matrix with n rows representing observations (e.g genes) and p columns representing variables (e.g samples).} \item{nbComp}{The number of components to be extracted.} \item{alg.type}{If \code{alg.type="parallel"} the components are extracted simultaneously (the default), if \code{alg.type="deflation"} the components are extracted one at a time, see \code{\link[fastICA]{fastICA}}.} \item{fun}{The functional form of the G function used in the approximation to neg-entropy (see 'details' of the help of function \code{\link[fastICA]{fastICA}}).} \item{maxit}{The maximum number of iterations to perform.} \item{tol}{A positive scalar giving the tolerance at which the un-mixing matrix is considered to have converged.} \item{...}{Additional parameters for \code{fastICA} and \code{JADE}} } \value{ A list, see outputs of \code{\link[fastICA]{fastICA}} and \code{\link[JADE]{JADE}}. This list includes at least three elements: \describe{\item{A}{the estimated mixing matrix} \item{S}{the estimated source matrix}, item{W}{the estimated unmixing matrix}} } \description{ This function performs ICA decomposition of a matrix using functions \code{\link[fastICA]{fastICA}} and \code{\link[JADE]{JADE}}. } \details{ See details of the functions \code{\link[fastICA]{fastICA}} and \code{\link[JADE]{JADE}}. } \examples{ set.seed(2004); M <- matrix(rnorm(5000*6,sd=0.3),ncol=10) M[1:10,1:3] <- M[1:10,1:3] + 2 M[1:100,1:3] <- M[1:100,1:3] +1 resJade <- runICA(X=M, nbComp=2, method = "JADE", maxit=10000) } \author{ Anne Biton }