R/edgeListFunctions.R

In sandraTL/PathQuantPadigm: Pathway Analysis with distance between genes and metablites

#'Function fractioning reaction list from every gene from KGML file
#'
#'
#'exemple : id R1... R2... R3... ko
#' -> id R1 ko
#' -> id R2 ko
#' -> id R3 ko
#'
#' @param data frame des reactions extraites du KGML en listes
#' @keywords  kegg
#' @examples completeEdgeList(edgeDataFrame)

unlistEdgeReactionCol <- function(edgeDataFrame){

    s <- strsplit(as.vector(edgeDataFrame$reactions), " ");
    edgeDataFrame <- data.frame(
                       kgmlId = rep(edgeDataFrame$kgmlId, sapply(s, length)),
                       reactions = unlist(s),
                       type = rep(edgeDataFrame$type, sapply(s, length)),
                       ko = rep(edgeDataFrame$ko, sapply(s, length)))

    return <- edgeDataFrame;


}


correctReactionString <- function(edgeDF){

    edgeDF <- lapply(edgeDF,
                           function (x) gsub("rn:","",x))

    return <- edgeDF;

}

#'Since it is not possible to have the related gene when parsing the
#'reaction nodes in the KGML. I had to parse de reaction nodes and the
#'gene entry nodes separatly and then combinde the 2 with the information
#'needed.
#'
#'the results gives a data.frame(substrateId, productId, subtrateName,
#'productName, reactionId, reactionName, ko(gene))
#'
#' @param id of the explored pathway
#' @keywords reaction data.frame
#' @examples finalReactionEdgeDF(pathwayId)

finalReactionEdgeDF <- function(pathwayId){

  #  print("finalReactionEdgeDF")

    edgeDF <- getListEdgeFromGeneKGML(pathwayId);
    reactionDF <- getListReactionFromKGML(pathwayId);
    reactionDF <- as.data.frame(lapply(reactionDF,
                                       function(X) unname(unlist(X))));

    mergeDF <-  merge(reactionDF, edgeDF, by="reactionId");
    mergeDF <- mergeDF[ -c(8,9)];
    mergeDF <- mergeDF[ c(2,3,4,5,1,6,7,8)];

    return <- mergeDF;

}