docs: small updates/fixes in documentation

R/MsBackend.R

@@ -187,9 +187,9 @@
 #'     parameter `spectraVariables` and in the same order.
 #'
 #' @param y For `cbind2()`: A `data.frame` or `DataFrame` with the
-#'     spectra variables to be added to the backend. Need to be of the same
-#'     length as the number of spectra in the backend. The number of rows and
-#'     their order has to match the number of spectra and their order in x.
+#'     spectra variables to be added to the backend. The number of rows of `y`
+#'     and their order have to match the number of spectra and their order
+#'     in `x`.
 #'
 #' @param x Object extending `MsBackend`.
 #'
@@ -318,11 +318,11 @@
 #'   `dropNaSpectraVariables()` might still show columns containing `NA` values
 #'   for *core* spectra variables.
 #'
-#' - `cbind2()`: allows to appends multiple spectra variables to the backend at
-#'   once. The `Spectra` and the values for the new spectra variables have to
-#'   be in a matching order. Replacing existing spectra variables is not
-#'   supported through this function. For a more controlled way of adding
-#'   spectra variables, the `joinSpectraData()` should be used.
+#' - `cbind2()`: allows to appends multiple new spectra variables to the
+#'   backend at once. The values for the new spectra variables have to
+#'   be in the same order as the spectra in `x`. Replacing existing spectra
+#'   variables is not supported through this function. For a more controlled
+#'   way of adding spectra variables, the `joinSpectraData()` should be used.
 #'
 #' - `centroided()`, `centroided<-`: gets or sets the centroiding
 #'   information of the spectra. `centroided()` returns a `logical`
@@ -1044,7 +1044,7 @@ setMethod("cbind2", signature = c("MsBackend", "dataframeOrDataFrameOrmatrix"),
           function(x, y = data.frame(), ...) {
     if (is(y, "matrix"))
         y <- as.data.frame(y)
-    if (any(colnames(spectraData(x)) %in% colnames(y)))
+    if (any(spectraVariables(x) %in% colnames(y)))
         stop("spectra variables in 'y' are already present in 'x' ",
              "replacing them is not allowed")
     if (nrow(y) != length(x))

R/MsBackendDataFrame.R

@@ -575,7 +575,7 @@ setMethod("cbind2", signature = c("MsBackendDataFrame",
           function(x, y = data.frame(), ...) {
               if (is(y, "matrix"))
                   y <- as.data.frame(y)
-              if (any(colnames(spectraData(x)) %in% colnames(y)))
+              if (any(spectraVariables(x) %in% colnames(y)))
                   stop("spectra variables in 'y' are already present in 'x' ",
                        "replacing them is not allowed")
               if (nrow(y) != length(x))

R/MsBackendMemory.R

@@ -678,7 +678,7 @@ setMethod("cbind2", signature = c("MsBackendMemory",
           function(x, y = data.frame(), ...) {
               if (is(y, "matrix"))
                   y <- as.data.frame(y)
-              if (any(colnames(spectraData(x)) %in% colnames(y)))
+              if (any(spectraVariables(x) %in% colnames(y)))
                   stop("spectra variables in 'y' are already present in 'x' ",
                        "replacing them is not allowed")
 

R/Spectra.R

@@ -1465,14 +1465,12 @@ setReplaceMethod("[[", "Spectra", function(x, i, j, ..., value) {
 #'   the [applyProcessing()] function.
 #'
 #' - `cbind2()`: Appends multiple spectra variables from a `data.frame`,
-#'   `DataFrame` or `matrix` to the `Spectra`  object at once. It does so
-#'   *blindly* (e.g. do not check rownames compatibility) and is therefore at
-#'   the risk of the user. The function also does not allow to replace existing
-#'   spectra variables. For a more  controlled way of adding spectra
-#'   variables, the `joinSpectraData()`  should be used. It will return a
-#'   `Spectra` object with the appended spectra variables. `cbind2()` does
-#'   check however that the number of rows of the `data.frame` or `DataFrame`
-#'   matches the number of spectra in the `Spectra` object.
+#'   `DataFrame` or `matrix` to the `Spectra` object at once. The order of
+#'   the values (rows) in `y` has to match the order of spectra in `x`. The
+#'   function does not allow to replace existing spectra variables. `cbind2()`
+#'   returns a `Spectra` object with the appended spectra variables. For a more
+#'   controlled way of adding spectra variables, see the `joinSpectraData()`
+#'   function.
 #'
 #' - `combineSpectra()`: combines sets of spectra (defined with parameter `f`)
 #'   into a single spectrum per set aggregating their MS data (i.e. their
@@ -1696,7 +1694,7 @@ setMethod("cbind2", signature(x = "Spectra",
                               y = "dataframeOrDataFrameOrmatrix"),
           function(x, y, ...) {
               x@backend <- cbind2(x@backend, y, ...)
-              })
+          })
 
 #' @rdname combineSpectra
 setMethod("split", "Spectra", function(x, f, drop = FALSE, ...) {