R/import.R

In compbiomed/BatchQC: Batch Effects Quality Control Software

#' This function creates a summarized experiment object from count
#' and metadata files uploaded by the user
#' @param counts counts dataframe
#' @param columndata metadata dataframe
#' @return a summarized experiment object
#' @import SummarizedExperiment
#' @import reader
#' @import EBSeq
#' @import utils
#'
#' @examples
#' data(protein_data)
#' data(protein_sample_info)
#' se_object <- summarized_experiment(protein_data, protein_sample_info)
#'
#' @export

summarized_experiment <- function(counts, columndata) {

    counts <- counts[rowSums(counts) > 0, ]
    mutual_sample <- intersect(colnames(counts), rownames(columndata))
    counts <- counts[, mutual_sample]
    columndata <- columndata[mutual_sample, ]

    se <- SummarizedExperiment(assays = list(counts = counts),
                                colData = columndata,
                                metadata = list(metadata = columndata))
    se <- se[which(rownames(se) != 'NA')]
    return(se)
}