R/readLibFile.R

In SwathXtend: SWATH extended library generation and statistical data analysis

###########################################################################
#' Load a spectrum library into a data frame
#' @param file A file of a spectrum library, in .txt or .csv format, can be .gz files.
#' @param format A character string denoting the file format. One of "peakview" (default) and "openswath"
#' @param type A character string denoting the file type. One of "spectrum" (default) and "hydro"
#' @param clean A logic value, representing if the library will be cleaned.
#' @param ... named arguments to be passed to the cleanLib function.
#' @return a data frame of the library with cleaning process
#' @examples 
#' file <- paste(system.file("files",package="SwathXtend"),"Lib1.txt",sep="/")
#' dat <- readLibFile(file)
############################################################################ 

readLibFile <- function(file, format = c("peakview", "openswath"),
                        type = c("spectrum", "hydro") ,clean = TRUE, ...)
{
  
  seps = c("\t",",")
  
  format <- match.arg(format)
  type <- match.arg(type)
  if(type == "spectrum"){
  if (grepl(".txt$",file) || grepl(".txt.gz$",file) ) 
  { 
    id <- 1
  } else if (grepl(".csv$",file) || grepl(".csv.gz$",file) ) {
    
    id <- 2 
  }  else {
    stop (paste(file, "have wrong file type !") )
  }
  
  
  
  sep <- seps[id] 

  dat <- read.delim2(file,sep=sep,header=TRUE,
                      stringsAsFactors=FALSE)
  
  if(ncol(dat) < 2){
    stop(paste(file, "wrong library file format!") )
  }
    
  dat <- try(canonicalFormat(dat, format = format) )
  
  if(inherits(dat,"try-error"))
    stop("Error with creating canonical format")
  
  dat <- try(cleanLib(dat, clean=clean, ...))
  
  if(inherits(dat,"try-error"))
    stop("Error with cleaning library")
  } else { ## Hydro
    dat <- read.delim2(file,sep=seps[1],header=TRUE,stringsAsFactor=FALSE)
  }    
  dat
  
}