Add argument msLevel to chromatogram,XCMSnExp (issue #205)

- Add argument msLevel to chromatogram,XCMSnExp.

DESCRIPTION

@@ -14,7 +14,7 @@ Depends:
     methods,
     Biobase,
     BiocParallel (>= 1.8.0),
-    MSnbase (>= 2.3.9)
+    MSnbase (>= 2.3.10)
 Imports:
     mzR (>= 1.1.6),
     BiocGenerics,

R/methods-XCMSnExp.R

@@ -1918,6 +1918,9 @@ setMethod("featureValues",
 #'     Details and Notes sections below). Use \code{missing = 0} to resemble the
 #'     behaviour of the \code{getEIC} from the \code{old} user interface.
 #'
+#' @param msLevel \code{integer} specifying the MS level from which the
+#'     chromatogram should be extracted. Defaults to \code{msLevel = 1L}.
+#' 
 #' @return \code{chromatogram} returns a \code{\link{Chromatograms}} object with
 #'     the number of columns corresponding to the number of files in
 #'     \code{object} and number of rows the number of specified ranges (i.e.
@@ -1987,7 +1990,8 @@ setMethod("featureValues",
 setMethod("chromatogram",
           signature(object = "XCMSnExp"),
           function(object, rt, mz, adjustedRtime = hasAdjustedRtime(object),
-                   aggregationFun = "sum", missing = NA_real_) {
+                   aggregationFun = "sum", missing = NA_real_,
+                   msLevel = 1L) {
               ## Coerce to OnDiskMSnExp.
               if (adjustedRtime)
                   adj_rt <- rtime(object, adjusted = TRUE)
@@ -1998,7 +2002,7 @@ setMethod("chromatogram",
               }
               chromatogram(object, rt = rt, mz = mz,
                            aggregationFun = aggregationFun,
-                           missing = missing)
+                           missing = missing, msLevel = msLevel)
           })
 
 #' @rdname XCMSnExp-class

inst/NEWS

@@ -1,6 +1,9 @@
 CHANGES IN VERSION 2.99.7
 -------------------------
 
+USER VISIBLE CHANGES:
+- Add parameter msLevel to chromatogram,XCMSnExp method (issue #205).
+
 BUG FIXES:
 - Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto.
 - Merge with BioC git after transition