quickfix to read_CoreMS_data vignette to allow use of iso_cols in as.…

…CoreMSData

DESCRIPTION

@@ -45,4 +45,4 @@ Suggests:
     viridis,
     DT
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

R/as.CoreMSData.R

@@ -28,15 +28,10 @@
 #'   column containing the monoisotopic index in \code{all_data}
 #' @param mf_cname a character string specifying the name of the column
 #'   containing the molecular formula in \code{all_data}
-#' @param c13_cname a character string specifying the name of the column
-#'   containing the C13 logical indicator in \code{all_data}
-#' @param s34_cname a character string specifying the name of the column
-#'   containing the S43 logical indicator in \code{all_data}
-#' @param o18_cname a character string specifying the name of the column
-#'   containing the O18 logical indicator in \code{all_data}
-#' @param n15_cname a character string specifying the name of the column
-#'   containing the N15 logical indicator in \code{all_data}
-#'
+#' @param iso_cols a character vector specifying columns indicating the presence
+#'  of isotopic peaks, e.g. a column "13C" with T/F specifying the presence of
+#'  13C.  Defaults to \code{c("13C", "18O", "15N", "34S")}.
+#' 
 #' @return `CoreMSData` object, consisting of a list of two data frames
 #' 
 #' @author Natalie Winans
@@ -93,7 +88,7 @@ as.CoreMSData <- function(all_data,
 
   # check that all isotopic peaks are indicated by isotopic columns and correct if not
   iso_mf_peaks <- monoiso_data %>%
-    dplyr::filter(stringr::str_detect(.data[[mf_cname]], "13C|18O|15N|34S"))
+    dplyr::filter(stringr::str_detect(.data[[mf_cname]], paste(iso_cols, collapse="|")))
 
   if (nrow(iso_mf_peaks) > 0) {
     iso_data <- rbind(iso_data, iso_mf_peaks)

vignettes/read_CoreMS_data.Rmd

@@ -57,7 +57,7 @@ dat %>%
 The next step is to convert the `CoreMSrbind` object into a `CoreMSData` object using the function `as.CoreMSData`. The arguments for this function are the `data.frame` output by the function `read_CoreMS_data` and, optionally, the names of the columns corresponding to mass-to-error ratio (m/z), peak height, mass error, confidence score, molecular formula, and other peak metadata. The default values for these parameters are set to the column names in typical CoreMS output. The column names corresponding to isotope columns C13, S34, O18, and N15 should be included if and only if present in the dataset. In this case, we will include names for the C13 and O18 columns.
 
 ```{r}
-cmsDat <- as.CoreMSData(dat, c13_cname = "13C", o18_cname = "18O")
+cmsDat <- as.CoreMSData(dat)
 ```
 
 The `CoreMSData` object consists of a list of two `data.frames`, `monoiso_data` and `iso_data`, containing the monoisotopic peaks and isotopic peaks, respectively. At this time, the isotopic peaks are not used for downstream analyses.