R/combineGenes.R

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

#' @title combineGenes
#' @description Combines miR and mRNA data into one dataframe. Input columns
#' should be written as : timepoint.DifferentialExpressionResultType e.g.
#' D1.log2fc or H6.adjPval. Column names should be the same for miR and mRNA
#' data. If a more detailed explanation of column nomenclature is needed please
#' read the vignette. combineGenes is essential for combined analysis of miR-mRNA
#' data. If using separate analysis, there is no need to use combineGenes.
#' @param MAE Input MAE which stores results from combineGenes. It is
#' recommended to use the MAE which was used in startObject.
#' @param miR_data microRNA dataframe. Rows should be genes, columns are DE
#' results and time point. This should be the stored as an assay within the
#' MAE used in the startObject function.
#' @param mRNA_data mRNA dataframe. Rows should be genes, columns are DE results
#' and time point. This should be the stored as an assay within the MAE used in
#' the startObject function.
#' @return A dataframe with combined miR and mRNA data. Will be stored as an
#' assay in the input MAE.
#' @export
#' @importFrom gtools mixedsort
#' @usage combineGenes(MAE, miR_data, mRNA_data)
#' @examples
#' library(org.Mm.eg.db)
#'
#' data(mm_miR)
#'
#' data(mm_mRNA)
#'
#' MAE <- startObject(miR = mm_miR, mRNA = mm_mRNA)
#'
#' MAE <- combineGenes(MAE = MAE, miR_data = assay(MAE, 1),
#'                     mRNA_data = assay(MAE, 2))
combineGenes <- function(MAE, miR_data, mRNA_data){

    if (missing(MAE)) stop('MAE is missing. Add MultiAssayExperiment to store the output of combineGenes. Please use the startObject function first.')

    if (missing(miR_data)) stop('miR_data is missing. Add dataframe of miR data. Rows should be genes, columns are DE results and time point. Please use the startObject function first. Output of the startObject function will be stored as assays within the MAE used in the startObject function.')

    if (missing(mRNA_data)) stop('mRNA_data is missing. Add dataframe of mRNA data. Rows should be genes, columns are DE results and time point. Please use the startObject function first. Output of the startObject function will be stored as assays within the MAE used in the startObject function.')

    # Extract the miR and mRNA data
    miR_data <- as.data.frame(miR_data)

    mRNA_data <- as.data.frame(mRNA_data)

    # Order them based on time point and result type
    miR_order <- gtools::mixedsort(names(miR_data))

    mRNA_order <- gtools::mixedsort(names(mRNA_data))

    # New order is how both data sets should be ordered
    miR_data <- miR_data[miR_order]

    mRNA_data <- mRNA_data[mRNA_order]

    genetic_data <- as.data.frame(rbind(miR_data, mRNA_data))

    # Combine with MAE object
    MAE <- suppressWarnings(c(MAE, suppressMessages(MultiAssayExperiment(experiments = list(
                                              "genetic_data" = genetic_data)))))

    return(MAE)
}