R/wikiMatrix.R

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

#' @title wikiMatrix
#' @description Creates a matrix which shows how many genes from the input mRNA
#' and miRNA data are found in each wikipathway, for a specific species.
#' @param MAE MultiAssayExperiment which will store the output of
#' wikiMatrix. It is recommended that the MAE object which stores output from
#' the wikiList function.
#' @param ID_list List of lists of entrez gene IDs or ensembl gene IDs stored
#' as strings. This is the output of the eNames function and is stored as
#' metadata in the MAE used in the eNames function.
#' @param wp_list List of lists containing wikipathways with entrez gene IDs or
#' ensembl IDs as strings. This is the output of the wikiList function and is
#' stored as metadata in the MAE used in the wikiList function.
#' @return A matrix showing which genes are found in each time points for
#' each pathway. Output will be stored as an assay in the input MAE.
#' @export
#' @usage wikiMatrix(MAE, ID_list, wp_list)
#' @examples
#' MAE <- MultiAssayExperiment()
#'
#' metadata(MAE)[["ID_list"]] <- e_list_mouse
#'
#' metadata(MAE)[["w_list"]] <- w_list_mouse[1:10]
#'
#' MAE <- wikiMatrix(MAE, ID_list = metadata(MAE)[[1]],
#'                   wp_list = metadata(MAE)[[2]])
wikiMatrix <- function(MAE, ID_list, wp_list){

    if (missing(MAE)) stop('MAE is missing. Add MAE which will store the results of wikiMatrix. Please use the eNames and wikiList functions first.')

    if (missing(ID_list)) stop('ID_list is missing. Add list of lists of gene IDs. Please use the eNames function before using wikiMatrix. Output of eNames should be stored as metadata within the MAE used in the eNames function.')

    if (missing(wp_list)) stop('wp_list is missing. Add list of lists of wikipathways and associated entrezgene or ensembl IDs. Please use the wikiList function before using wikiMatrix. Output of wikiList should be stored as metadata within the MAE used in the wikiList function.')

    # Convert list into matrix
    wmat <- sapply(wp_list, function(x) {
        sapply(ID_list, function(y) sum(x %in% y))})

    L <- lapply(wp_list, function(x){length(x)})

    wmat2 <- as.data.frame(rbind(wmat, Total = unlist(L)))

    MAE2 <- suppressMessages(MultiAssayExperiment(list("wikimatrix" = wmat2)))

    MAE <- c(MAE, MAE2)

    return(MAE)
}