#' Convert Nanostring RCC Files to Matrix Form
#'
#' \code{convert_RCC_to_mat} converts the RCC files in a directory into a
#' matrix.
#'
#' @param rcc.dir The path to the directory holding the RCC files
#' @return Matrix containing the raw nanostring count data of each RCC file
#' @author Stacy Hung
#' @export
convert_RCC_to_mat <- function(rcc.dir) {
if (!requireNamespace("NanoStringNorm", quietly = TRUE)) {
stop("NanoStringNorm needed for this function to work. Please install it.",
call. = FALSE)
}
data.raw <- NanoStringNorm::read.markup.RCC(rcc.dir)
data.norm <- NanoStringNorm::NanoStringNorm(data.raw, OtherNorm = "none");
data.norm.mat <- data.norm$normalized.data
# Remove Non-Expression Data Columns
data.norm.mat.2 <- data.norm.mat[, 4:length(data.norm.mat)]
data.norm.mat.2
}
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