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#calculatePI:
#' A function for calculating proliferative index from variance stabalized RNA-seq data in the ProliferativeIndex package
#'
#' This function allows the user to read in data for subsequent proliferative index calculation and analysis
#' @param userObject Output from ProliferativeIndex readDataForPI function
#' @export
#' @examples
#' calculatePI(exReadDataObj)
calculatePI<-function(userObject){
dataframePIvst<-subset(userObject$vstData, rownames(userObject$vstData) %in% metaPCNA2)
vstPI<-apply(dataframePIvst, 2, stats::median)
print(paste("vstData contained ", nrow(dataframePIvst), "/131 of the PI-associated genes", sep=""))
invisible(vstPI)
}
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