#' Get indicies of spectra per plaque ID
#'
#' @param pp plaque picker result list. See \code{plaquePicker}
#' @param ID vector of ID, set to NA to return all Indicies associated with any clump.
#' @param mzValue mzValue to ID is refering to. By default the unified IDs are used but this can also be overwritten by entering a specific mz.
#'
#' @return
#' vector of indicies refering to the spectra in the MALDIquant spectra list used to construct the ion images used.
#' @export
get_IdxFromID <- function(pp, ID, mzValue = "unified") {
mzValue <- as.character(mzValue)
if(length(mzValue) > 1) {
stop("mzValue needs to be length == 1\n")
}
if(!mzValue %in% c(get_mzValues(pp), "unified")) {
stop("mzValue not contained in pp\n")
}
if(any(is.na(ID))) {
cat("ID set to NA. Returning all indicies associated with any clump.\n")
ID <- 1:length(pp[[mzValue]][["spectraIdx"]])
}
idx <- lapply(ID, function(x) {
pp[[mzValue]][["spectraIdx"]][[x]]
})
return(unlist(idx))
}
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