#' @title check13c
#'
#' @param windowData - the mz intensity table making up the observations of a
#' given mass spectra.
#' @param ppm - error window used to identify 13C peaks
#'
#' @description This function checks if the scan with the parent ion has a
#' 13C feature. If it does, it remove the 13C feature from the scan window and
#' combines the purity. The new table tells us if we need to fix the ms2 should
#' be corrected for contamination.
#'
#' @importFrom dplyr %>%
#' @return The windowData table with an additional column used to indicate
#' if the data has a 13C peak that could be contamination the ms2 scan.
check13c <- function(windowData, ppm) {
windowData$has13C <- F
if(nrow(windowData) == 1) {
return(windowData)
}
if(abs((windowData$mzs[1] + 1) - windowData$mzs[2])/windowData$mzs[1] * 10^6 < ppm*2) {
newPurityScore <- sum(windowData$purity[c(1,2)])
windowData$purity[c(1,2)] <- newPurityScore
windowData$intensity[c(1,2)] <- sum(windowData$intensity[c(1,2)])
windowData <- windowData[-2,]
windowData$has13C[1] <- T
}
return(windowData)
}
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