add chromPeaks information to the Spectra output of chromPeakSpectra

sneumann · Nov 20, 2024 · cd7e00c · cd7e00c
1 parent 7c9e7d3
commit cd7e00c
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R
@@ -793,7 +793,8 @@
                                                  "largest_bpi"),
                                    msLevel = 2L, expandRt = 0, expandMz = 0,
                                    ppm = 0, skipFilled = FALSE,
-                                   peaks = integer(), BPPARAM = bpparam()) {
+                                   peaks = integer(), peaksInfo = c("rt", "mz"),
+                                   BPPARAM = bpparam()) {
     method <- match.arg(method)
     pks <- .chromPeaks(x)[, c("mz", "mzmin", "mzmax", "rt",
                               "rtmin", "rtmax", "maxo", "sample")]
@@ -830,6 +831,7 @@
             ids <- rep(rownames(pk), lengths(idx))
             res <- sp[unlist(idx)]
             res$peak_id <- ids
+            res2@backend@spectraData <- cbind(res2@backend@spectraData, info)
             res
         },
         MoreArgs = list(msLevel = msLevel, method = method),

diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
@@ -515,6 +515,10 @@
 #'     indicating the identified chromatographic peaks. Only a single color
 #'     is supported. Defaults to `peakCol = "#ff000060".
 #'
+#' @param peaksInfo For `chromPeakSpectra`: `character`  vector of additional
+#'    information from `chromPeaks()` to be added to the spectra object. The
+#'    columns names will be appended with "peaks_".
+#'
 #' @param ppm For `chromPeaks` and `featureDefinitions`: optional `numeric(1)`
 #'     specifying the ppm by which the m/z range (defined by `mz` should be
 #'     extended. For a value of `ppm = 10`, all peaks within `mz[1] - ppm / 1e6`
@@ -1228,7 +1232,7 @@ setMethod(
     function(object, method = c("all", "closest_rt", "closest_mz",
                                 "largest_tic", "largest_bpi"),
              msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0,
-             skipFilled = FALSE, peaks = character(),
+             skipFilled = FALSE, peaks = character(), peaksInfo = c("rt", "mz")
              return.type = c("Spectra", "List"), BPPARAM = bpparam()) {
         if (hasAdjustedRtime(object))
             object <- applyAdjustedRtime(object)
@@ -1244,7 +1248,7 @@ setMethod(
         else pkidx <- integer()
         res <- .mse_spectra_for_peaks(object, method, msLevel, expandRt,
                                       expandMz, ppm, skipFilled, pkidx,
-                                      BPPARAM)
+                                      peaksInfo, BPPARAM)
         if (!length(pkidx))
             peaks <- rownames(.chromPeaks(object))
         else peaks <- rownames(.chromPeaks(object))[pkidx]