R/cleanLib.R

In SwathXtend: SWATH extended library generation and statistical data analysis

###########################################################################
#' Spectrum library cleanining
#' @param datLib a data frame for a spectrum library
#' @param nomod a logic value, representing if the modified peptides and its
#' fragment ions will be removed. True (default) means will be removed.
#' @param nomc a logic value, representing if peptides with miss cleavages
#' are removed. Default vaue is False (not to remove).
#' @param intensity.cutoff A number value to specify cut off for relative 
#' intensity of fragment ions. Only ions with intensity higher than the
#' cut off value (default as 5) will be kept.
#' @param conf.cutoff A number value to specify cut off for precursor 
#' confidence. Only ions with confidence higher than the cut off value
#' (default as 0.99) will be kept.
#' @param enz A character string representing the enzyme which can be one of
#' "trypsin" (defalut), "gluc", or "chymotrypsin"
#' @return a data frame of a cleaned spectrum library by the specified
#' criteria
#' @examples 
#' file <- paste(system.file("files",package="SwathXtend"),"Lib1.txt",sep="/")
#' dat <- read.delim2(file,sep="\t",header=TRUE,stringsAsFactors=FALSE)
#' dat <- canonicalFormat(dat)
#' dat <- cleanLib(dat)
############################################################################                      

cleanLib <- function(datLib, clean=TRUE, intensity.cutoff=5,conf.cutoff=0.99,
                    nomod = FALSE, nomc = FALSE, enz=c("trypsin", "gluc", "chymotrypsin") )
{

  enz <- match.arg(enz)
  
  if(clean)
    dat.res <- datLib[as.numeric(datLib$relative_intensity)>
                       intensity.cutoff &
                       as.numeric(datLib$confidence) > 
                       conf.cutoff,]
  
  else   dat.res <- datLib
  
  
  if(nomod)
    if(length(grep("\\[",dat.res$modification_sequence))>0)
      dat.res <- dat.res[-grep("\\[",dat.res$modification_sequence),]
  if(nomc)
  
    dat.res <- dat.res[-sapply(dat.res$stripped_sequence, 
                               FUN=function(x){isMissCleavaged(x, enz)}),]

  dat.res
}