#' Transform intensity values in a gradient of color from green to red.
#' @author Simon J Pelletier
#' @import GEOquery
#' @param exprset Expression set containing all the information on a dataset
#' @return A vector of colors. The darkest green values are the lowest and the darkest red values are the highest.
#' @keywords comparisons
#' @seealso
#' \code{\link[GEOquery]{getGEO}}
#' \code{\link[Biobase]{ExpressionSet}}
#' @examples
#' gset <- getGEO('GSE61276', GSEMatrix =TRUE) #GSE61276 GSE12654
#' exprset <- gset[[1]]
#' comparisons <- comparisonsPheno(exprset)[[1]]
#' comparisonsTable <- comparisonsPheno(exprset)[[2]]
#' @export
comparisonsPheno = function(exprset){
comparisons_table <- pData(exprset)
comparisons = apply(comparisons_table,2,function(x){
paste(unique(x),collapse="\\")
})
comparisons2 = NULL
j<-1
for(i in 1:length(comparisons)){
if(length(strsplit(comparisons[i],"\\\\")[[1]]) > 1 & length(strsplit(comparisons[i],"\\\\")[[1]]) < ncol(exprs(exprset))){
comparisons2[j] = comparisons[i]
names(comparisons2)[j] = names(comparisons)[i]
j<-j+1
} else {
comparisons_table = comparisons_table[,-j]
}
}
comparisons2 = comparisons2[!duplicated(comparisons2)]
comparisons_table = comparisons_table[!duplicated(lapply(comparisons_table,summary))]
return(list(comparisons2,comparisons_table))
}
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