R/check_software_input.R

In svalvaro/MQanalyser: Analyse the proteomics LC-MS/MS data from MaxQuant.

#' Maxquant or spectronaut
#'
#' @param file
#' @return maxquant or spectrounaut
#' @export
#'
#' @examples
check_software_input <- function(file){

    # If no data frame was loaded, return NULL
    if (!is.data.frame(file)) {
        return(NULL)
    }

    # To check if the input is coming from MaxQuant:

    if ('Protein.IDs' %in% base::colnames(file) &&
        'Protein.names'%in% base::colnames(file) &&
        'Majority.protein.IDs' %in% base::colnames(file)) {

        software_used <- 'MaxQuant'

    } else if('PG.ProteinGroups' %in% base::colnames(file) &&
              'PG.ProteinDescriptions' %in% base::colnames(file)) {

        software_used <- 'Spectronaut'
    }else if('Protein ID' %in% colnames(file) &&
             'Protein Existence' %in% colnames(file)){
        software_used <- 'MSFragger'
    }

    message(paste0(software_used, ' software detected'))

    return(software_used)
}