R/addPrefix.R

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

#' @title addPrefix
#' @description Adds 'miR_' or 'mRNA_' genetypes to colnames of dataframes.
#' Resulting colnames should be in the following naming system:
#' 'genetype_timepoint.resulttype'.
#' This function is essential for separate analysis of miR-mRNA DE data. If
#' using the combined analysis, there is no need to use addPrefix.
#' @param MAE MultiAssayExperiment to store output of addPrefix.
#' It is recommended to use the MAE object which stores output from startObject.
#' @param gene_df Dataframe of mRNA or miR results from differential expression
#' analysis. Will be stored as an assay within the MAE used in the startObject
#' function.
#' @param prefixString Prefix to be added e.g. "miR" or "mRNA".
#' @return Dataframe which has a specific prefix infront of each column name.
#' Will be stored as an assay in the input MAE.
#' @export
#' @usage addPrefix(MAE, gene_df, prefixString = '')
#' @examples
#' data(mm_miR)
#'
#' data(mm_mRNA)
#'
#' MAE <- startObject(miR = mm_miR, mRNA = mm_mRNA)
#'
#' MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 1),
#'                  prefixString = "miR")
#'
#' MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 2),
#'                  prefixString = "mRNA")
addPrefix <- function(MAE, gene_df, prefixString){
    if (missing(MAE)) stop('MAE is missing. Add MAE to store output of addPrefix. Please use startObject first. ')

    if (missing(gene_df)) stop('gene_df is missing. Add dataframe containing miR or mRNA DE data. Please use startObject first. Output of startObject should be stored as assays within the MAE used in startObject.')

    if (missing(prefixString)) stop('prefixString is missing. Add a prefix string e.g. "miR" or "mRNA."')

    gene_df <- as.data.frame(gene_df)

    # If gene_df already has the prefixString as a prefix then == NO
    ifelse(test = grepl(prefixString, names(gene_df)) == FALSE,
            yes = colnames(gene_df) <- paste(prefixString,
                                             colnames(gene_df),
                                             sep = '_'),
            no = print('miR/mRNA info is fine'))
    # Add to MAE
    MAE2 <- suppressMessages(MultiAssayExperiment(experiments = list(
                                                                x = gene_df)))

    # Add prefix to column names
    x <- paste(prefixString, "p", sep = "_")

    names(MAE2) <- x

    MAE <- c(MAE, MAE2)

return(MAE)
}