R/getITtime.R

In wilsontom/rawReadeR: Read Thermo .RAW files in R

#' Get Ion Injection Time
#'
#' Get the ion injection time (IT) for each scan in a given range
#'
#' @param filename a \code{.raw} file
#' @param scans a numeric vector of scan numbers to extract
#' @return a numeric vector of the ion injection time for each scan
#' 
#' @author Tom Wilson \email{tpw2@@aber.ac.uk}
#' @export
#' @examples
#' \dontrun{
#'	getITtime(QC.raw, scans = c(2:24)	
#'	}
#'
getITtime <- function(filename, scans = c())
	{
	options(digits = 15)
	
	IT <- sapply(scans, function(x)(shell(paste(system.file("bin/GetIT.exe", package = "rawReadeR"), filename, x, sep = " "), intern = TRUE)))
	
	if(length(grep("::", IT)) == length(IT)){
		IT <- gsub("Ion Injection Time \\(ms\\)::", "", IT)
	}else{
		IT <- gsub("Ion Injection Time \\(ms\\):", "", IT)
	}		
	return(as.numeric(IT))
	}