R/findBeta.R

In ypssc: Yeast-Proteome Secondary-Structure Calculator

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# >>
#' @title Beta Sheet Calculator
#' @description Form bottom-up proteomics data of proteins (peptides), this function determines the sections of proteins (in
#'   percentage) with beta-sheet, structure.
#' @param pathFileInput Path of the input csv file generated from MaxQuant. \cr
#'   \cr
#'   MaxQuant is a quantitative proteomics software designed to analyze large mass-spectrometric data. The input of MaxQuant is a
#'   raw file (.raw) from high-resolution mass spectrometers. After analysis of the raw file in MaxQuant, the program generates a
#'   folder named “combined”. \cr
#'   \cr
#'   In this folder there is another folder named “txt” which contains many files with text format (.txt). One of the files called
#'   “peptides” which is the input of the ypssc to calculate secondary structures. ypssc has been designed such a way that can
#'   analyzed and extract information regarding the sample regardless of the name that user chosen for the sample.
#' @param pathDirOutput Path of the directory to which the output files will be generated.
#' @param ... (for developer use only)
#' @return The output of the program is a csv file (.csv) that contains 5 columns, and the number of rows depends on the number of
#'   proteins in the sample. \cr
#'   \cr
#'   First column contains the ID of the identified alpha-helix proteins in the sample, second column contains the number of identified
#'   amino acids from the corresponding protein, third column contains number of identified amino acids with secondary structure,
#'   fourth column contains the number of amino acids that the protein originally has in the SSDYP, and fifth column contains the
#'   number of amino acids with beta-sheet that the protein originally has in the SSDYP. \cr
#'   \cr
#'   These columns should provide all information that the user needs to know about the protein and its structural information as
#'   well as structural information about the parts of the protein that has been identified in the sample. \cr
#'   \cr
#'   In addition, it also generates 4 more '.csv' files. \cr
#'   1. The no. of proteins found in the sample. \cr
#'   2. The no. of peptides found in the sample. \cr
#'   3. The no. of amino acids for each protein in database. \cr
#'   4. It is the input file from MaxQuant that's been cleaned up for the sole purpose of calculating secondary structures.
#' @examples
#' \dontrun{
#' findBeta( pathFileInput = "some/path/to/inputFile.csv",
#'           pathDirOutput = "some/path/to/outputDir/" )
#'
#' findBeta()
#' }
#' @seealso [`findSecondary`], [`findAlpha`], [`findChain`]
#' @export
# <<
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##################################### findBeta() ###################################################################################
# >>
findBeta = function( pathFileInput = NULL,
                     pathDirOutput = NULL, ... ) {

    startTime          = Sys.time()
    originalWorkingDir = getwd()
    if ( length(c(...)) != 0  ) { isTest = c(...)[1] } else { isTest = FALSE }

    # Print intro >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    Err$box( "Beta Sheet Calculator started..." )

    # Checking if 'pathFileInput' is provided or exists >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    pathFileInput = checkFileInput( pathFileInput )

    # Checking if 'pathDirOutput' is provided >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    pathDirOutput = checkDirOutput( pathDirOutput )

    # Reading the input sample file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    dataFileInput     = readFileInput( pathFileInput, isTest )
    df                = dataFileInput$df
    sampleNames       = dataFileInput$sampleNames
    sampleNamesUpdate = dataFileInput$sampleNamesUpdate

    # Creating output folder >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    dateTimeCurrent = creatOutputDir( pathDirOutput, "beta" )

    # Removing the rows that are not needed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    df = removeRows( df, dateTimeCurrent, isTest )

    # Writing `dataBase_numOfAA` >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    write.csv( dataBase_numOfAA,
               paste0( dateTimeCurrent, "_dataBase_numOfAA.csv" ),
               row.names = FALSE )

    # Alpha helix calculation for dataBase >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    calculationBetaSheet( df, sampleNames, sampleNamesUpdate, dateTimeCurrent )

    # End >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    updateUserSuccess(isTest)
    endTime   = Sys.time()
    timeTaken = endTime - startTime
    Err$note(0); Err$note( paste0( "Time taken for the ypssc run: ", format(timeTaken) ) )
    Err$note(0); Err$note(0)

    # Setting working directory back to original >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

    setwd( originalWorkingDir )

    return( invisible(NULL) )

}
# <<
##################################### findBeta() ###################################################################################
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