R/dcBuildInfoDataFrame.r

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

#' Function to build an object of the S4 class InfoDataframe from an input file
#'
#' \code{dcBuildInfoDataFrame} is supposed to build an object of of the S4 class \code{\link{InfoDataFrame}}, given an input file. This input file can, for example, contain the domain information. 
#'
#' @param input.file an input file used to build the object. For example, a file containing InterPro domains (InterPro) can be found in \url{http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt}. As seen in this example, the input file must contain the header (in the first row), and entries in the first column intend to be domain identities (and must be unique). Note: the file should use the tab delimiter as the field separator between columns
#' @param output.file an output file used to save the built object as an RData-formatted file. If NULL, this file will be saved into "InfoDataFrame.RData" in the current working local directory
#' @return 
#' Any use-specified variable that is given on the right side of the assigement sign '<-', which contains the built \code{dcBuildInfoDataFrame} object.
#' Also, an RData file specified in "output.file" is saved in the local directory.  
#' @note If there are no use-specified variable that is given on the right side of the assigement sign '<-', then no object will be loaded onto the working environment.
#' @export
#' @seealso \code{\link{InfoDataFrame}}
#' @include dcBuildInfoDataFrame.r
#' @examples
#' \dontrun{
#' # build an "InfoDataFrame" object that contains information on InterPro domains (InterPro)
#' InterPro <- dcBuildInfoDataFrame(input.file="http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt", output.file="InterPro.RData")
#' InterPro
#' }

dcBuildInfoDataFrame <- function(input.file, output.file="InfoDataFrame.RData")
{
    if(is.null(input.file) | is.na(input.file)){
        stop("The input file must be provided!\n")
    }
    
    if(is.null(output.file)){
        warnings("Since the output file is not provided, the function will use the default output file 'InfoDataFrame.RData'!\n")   
        output.file <- "InfoDataFrame.RData"
    }
    
    ## read the input file
    domain_info <- utils::read.delim(input.file, header=T, sep="\t")
    rownames(domain_info) <- domain_info[,1]
    domain_info <- domain_info[order(domain_info[,1]),] # order according to the first column
    
    x <- as(domain_info, "InfoDataFrame")

    # remove the RData extension 
    output.var <- gsub(".RData$", "", output.file, ignore.case=T, perl=T)
    output.var <- gsub(".RDat$", "", output.var, ignore.case=T, perl=T)
    output.var <- gsub(".RDa$", "", output.var, ignore.case=T, perl=T)
    
    do.call(assign, list(output.var, x))
    save(list=output.var, file=output.file)
    
    if(file.exists(output.file)){
        message(sprintf("An object of S4 class 'InfoDataFrame' has been built and saved into '%s'.", file.path(getwd(),output.file)), appendLF=T)
    }
    
    invisible(x)
}