R/Utils.R

In sandraTL/PathQuant: Annotation of gene-metabolite pairs using topology of KEGG metabolic pathway maps

#' Importing data from an XSLX file, in the context of this package, one of the
#' data to import is the association file.
#'
#' @param path to XSLX file.
#' @keywords data, import, XSLX, data frame, associations.
#' @export
#' @examples inputXLSXtoDF("file_path/fileName.xlsx")

importXLSXtoDF <- function(file, sheet.num = 1){

    # print("importXLSXtoDF")

    input_data = gdata::read.xls(file, sheet = sheet.num)

    return <- input_data;

}



#' Importing data from an txt file (with table separators),
#' in the context of this package, one of the
#' data to import is the association file.
#'
#' @param path to txt file.
#' @keywords data, import, txt, data frame, associations.
#' @export
#' @examples inputXLSXtoDF("file_path/fileName.xlsx")

importTXTtoDF <- function(file){

    # print("importTXTtoDF")

    input_data = read.table(file)

    return <- input_data;

}


#' Export results data of a data frame into a text files, for which each lines
#' separates the data from every data frame colum by tabulation. This text file
#' can be easily opened with excel.

#' @param a dataframe.
#' @keywords data, export, txt, dataframe.
#' @export
#' @examples exportDFtoTxt(dataFrame, exportFileName)

exportDFtoTxt <- function(export_data, exportNameFile){

    # print("exportDFtoTxt")


    exportNameFile = paste(exportNameFile, ".txt", sep = "");

    return <- write.table(export_data, exportNameFile, sep="\t")

}


#' get the shortest path between on specific association between one gene and
#' one metabolite

#' @param pathwayId KEGG Id of selected pathway.
#' @param gene KEGG Id.
#' @param Metabolite KEGG Id.
#' @param commonNames get KEGG's Common Names of the KEGG Id provided in the
#'        path results.
#' @keywords association, path.
#' @export
#' @examples getPath("hsa:01100","hsa:1373", "C00300", T)

#
# getPath <- function(pathwayId, gene, metabolite, commonNames = F){
#
#     print("getPath")
#
#     asso <- data.frame(gene = as.vector(gene),
#                        metabolite = as.vector(metabolite));
#
#       res <- getDistanceAsso(pathwayId, asso,F,F);
#       path <- res["path"]
#
#       if(commonNames == T){
#
#           path <-getPathCommonNames(path);
#       }
#
#      return <- path;
#
# }
#