From 7d169e4e36cf1b5c399721bc32f9616da2b5d3f9 Mon Sep 17 00:00:00 2001
From: jorainer <johannes.rainer@gmail.com>
Date: Fri, 22 Sep 2023 13:54:04 +0200
Subject: [PATCH] docs: add comment and documentation

---
 R/MsBackend.R          | 6 +++++-
 R/MsBackendDataFrame.R | 2 ++
 man/MsBackend.Rd       | 6 +++++-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/R/MsBackend.R b/R/MsBackend.R
index ae21e74c..79970a57 100644
--- a/R/MsBackend.R
+++ b/R/MsBackend.R
@@ -561,7 +561,11 @@
 #' `data`. The second parameter `peaksVariables` allows to define which columns
 #' in `data` contain *peak variables* such as the m/z and intensity values of
 #' individual peaks per spectrum. The default for this parameter is
-#' `peaksVariables = c("mz", "intensity")`.
+#' `peaksVariables = c("mz", "intensity")`. Note that it is not supported to
+#' provide either `"mz"` or `"intensity"`, if provided, both need to be
+#' present in the data frame. Alternatively, the function also supports a data
+#' frame without m/z and intensity values, in which case a `Spectra` without
+#' mass peaks is created.
 #'
 #' Suggested columns of this `DataFrame` are:
 #'
diff --git a/R/MsBackendDataFrame.R b/R/MsBackendDataFrame.R
index 4d2b71fb..424e64da 100644
--- a/R/MsBackendDataFrame.R
+++ b/R/MsBackendDataFrame.R
@@ -62,6 +62,8 @@ setMethod("backendInitialize", signature = "MsBackendDataFrame",
               if (!is(data, "DataFrame"))
                   stop("'data' has to be a 'DataFrame'")
               peaksVariables <- intersect(peaksVariables, colnames(data))
+              ## support either no m/z or intensity values provided, or both
+              ## have to be specified.
               if (sum(c("mz", "intensity") %in% peaksVariables) == 1L)
                   stop("Both \"mz\" and \"intensity\" peak variables ",
                        "need to be provided.")
diff --git a/man/MsBackend.Rd b/man/MsBackend.Rd
index c473147e..3d6a1ba5 100644
--- a/man/MsBackend.Rd
+++ b/man/MsBackend.Rd
@@ -779,7 +779,11 @@ subsequently initialized with the \code{backendInitialize} method, taking a
 \code{data}. The second parameter \code{peaksVariables} allows to define which columns
 in \code{data} contain \emph{peak variables} such as the m/z and intensity values of
 individual peaks per spectrum. The default for this parameter is
-\code{peaksVariables = c("mz", "intensity")}.
+\code{peaksVariables = c("mz", "intensity")}. Note that it is not supported to
+provide either \code{"mz"} or \code{"intensity"}, if provided, both need to be
+present in the data frame. Alternatively, the function also supports a data
+frame without m/z and intensity values, in which case a \code{Spectra} without
+mass peaks is created.
 
 Suggested columns of this \code{DataFrame} are:
 \itemize{