R/assessQuality.R

In PeteHaitch/RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis.

#' Quality assessment for cleaning procedures.
#'
#' \code{assessQuality} allows to assess the quality of cleaning procedures in the context
#' 	of correlations when the true underlying correlation structure is known. 
#' 
#' @param est A matrix of estimated gene expression values.
#' @param true A matrix of true correlations.
#' @param index A vector of indices of genes to be included in the assessment; if \code{index="all"}
#'	all genes are considered.
#' @param methods The method used for quality assessment; if \code{method="fnorm"} the Frobenius norm is used;
#' 	if \code{method="wrong.sign"} the percentage of wrongly estimated signs is calculated if \code{method="all"}
#'	both are calculated.   
#' @return \code{assessQuality} returns a vector of the requested quality assessments.
#'
#' @details
#' The Frobenius norm used for \code{assessQuality} has the following structure
#' 	\deqn{F=\frac{\|E-T\|^2}{s}}
#' 	Here, the parameter \eqn{E} and the parameter \eqn{T} denote the lower triangles of the estimated and true correlation
#' 	matrices, respectively. The parameter \eqn{s} denotes the number of elements in \eqn{E} and \eqn{T}.
#' @examples
#' Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 250, 100, check.input=FALSE)  
#' assessQuality(Y$Y, Y$Sigma, index=1:100, methods="wrong.sign")
#' assessQuality(Y$Y, Y$Sigma, index=1:100, method="fnorm")
#' @author Saskia Freytag
#' @export
assessQuality<-function(
								est, # estimated expression values in matrix
								true, # true correlation values in matrix
								index="all", # index of genes wanted for analysis
								methods=c("all", "fnorm", "wrong.sign") # methods
							){
	if (index[1]!="all"){
		est<-est[,index]
		true<-true[index,index]
	}
	
	est<-cor(est)	
						
	res<-vector(length=0)		
	# initialise result vector		
	
	if(any(methods=="fnorm"| methods=="all")){
		res<-sum((true[lower.tri(true)]-est[lower.tri(est)])^2)/length(true[lower.tri(est)])
		# calculation of Frobenius Norm based on lower triangle of matrices
	}	
	if(any(methods=="wrong.sign"| methods=="all")){
		neg<-which(true<0,arr.ind=T)
		# index of truly negative values
		pos<-which(true>0,arr.ind=T)
		# index of truly positive values
		res<-c(res,(sum(est[pos]<0) + sum(est[neg]>0))/length(true))
		# calculation of percentage of correlations with wrong sign
	}							
	if(length(res)==1){
		if(methods=="fnorm") {
		names(res)<-"fnorm"
		} else {names(res)<-"wrong.sign"}
	} else names(res)<-c("fnorm", "wrong.sign")
	
	return(res)							
}