tests: increase unit test coverage

R/AllGenerics.R

@@ -30,9 +30,9 @@ setGeneric("matchedData", function(object, ...)
 #' from `target` based on settings specified with `param` and returns the result
 #' from this as a [MatchedSpectra] object.
 #'
-#' @param query [Spectra] object with the (experimental) spectra.
+#' @param query [Spectra::Spectra] object with the (experimental) spectra.
 #'
-#' @param target spectral data to compare against. Can be another [Spectra].
+#' @param target MS data to compare against. Can be another [Spectra::Spectra].
 #'
 #' @param param parameter object containing the settings for the matching (e.g.
 #'     eventual prefiltering settings, cut-off value for similarity above which
@@ -44,8 +44,8 @@ setGeneric("matchedData", function(object, ...)
 #'
 #' @author Johannes Rainer
 #'
-#' @seealso [CompareSpectraParam()] for the comparison between [Spectra]
-#'     objects.
+#' @seealso [CompareSpectraParam()] for the comparison between
+#'     [Spectra::Spectra] objects.
 #'
 #' @export
 setGeneric("matchSpectra", function(query, target, param, ...)

R/CompAnnotationSource.R

@@ -17,7 +17,8 @@
 #' Objects extending `CompAnnotationSource` available in this package are:
 #'
 #' - [CompDbSource()]: annotation source referencing an annotation source in the
-#'   `[CompDb()]` format ( from the `CompoundDb` Bioconductor package).
+#'   `[CompoundDb::CompDb()]` format ( from the `CompoundDb` Bioconductor
+#'   package).
 #'
 #' Classes extending `CompAnnotationSource` need to implement the `matchSpectra`
 #' method with parameters `query`, `target` and `param` where `query` is
@@ -32,7 +33,8 @@
 #' This would also enable parallel processing of annotations as no e.g. database
 #' connection would have to be shared across processes.
 #'
-#' @param query for `matchSpectra`: [Spectra] object with the query spectra.
+#' @param query for `matchSpectra`: [Spectra::Spectra] object with the query
+#'   spectra.
 #'
 #' @param target for `matchSpectra`: object extending [CompAnnotationSource]
 #'   (such as [CompDbSource]) with the target (reference) spectra to compare

R/CompDbSource.R

@@ -6,11 +6,12 @@
 #'
 #' @description
 #'
-#' `CompDbSource` objects represent references to [CompDb] database-backed
-#' annotation resources. Instances are expected to be created with the dedicated
-#' construction functions such as `MassBankSource` or the generic
-#' `CompDbSource`. The annotation data is not stored within the object but will
-#' be accessed/loaded within the object's `matchSpectra` method.
+#' `CompDbSource` objects represent references to [CompoundDb::CompDb]
+#' database-backed annotation resources. Instances are expected to be
+#' created with the dedicated construction functions such as
+#' `MassBankSource` or the generic `CompDbSource`. The annotation data is
+#' not stored within the object but will be accessed/loaded within the
+#' object's `matchSpectra` method.
 #'
 #' New `CompDbSource` objects can be created using the functions:
 #'
@@ -149,7 +150,7 @@ setMethod(
 #'
 #' @rdname CompDbSource
 MassBankSource <- function(release = "2021.03", ...) {
-    if (!requireNamespace("AnnotationHub", quietly = TRUE))
+    if (!.is_available_annotation_hub())
         stop("'MassBankSource' requires the 'AnnotationHub' package.\n",
              "Please install it with 'BiocManager::install(",
              "\"AnnotationHub\")' and try again.")
@@ -163,3 +164,7 @@ MassBankSource <- function(release = "2021.03", ...) {
     fn <- unname(AnnotationHub::cache(res))
     CompDbSource(fn)
 }
+
+.is_available_annotation_hub <- function(x) {
+    requireNamespace("AnnotationHub", quietly = TRUE)
+}

R/Matched.R

@@ -20,8 +20,9 @@
 #' structures such as `SummarizedExperiments` or `QFeatures`. Combinations of
 #' all these different data types are also supported. Matches are represented
 #' between elements of one-dimensional objects, or rows for two-dimensional
-#' objects (including `SummarizedExperiment` or `QFeatures`). For [QFeatures()]
-#' objects matches to only one of the *assays* within the object is supported.
+#' objects (including `SummarizedExperiment` or `QFeatures`). For
+#' [QFeatures::QFeatures()] objects matches to only one of the *assays*
+#' within the object is supported.
 #'
 #' @section Creation and general handling:
 #'
@@ -142,8 +143,9 @@
 #'   extracted with `x$query` (`x$target`). More precisely, when
 #'   *query* (*target*) is a `SummarizedExperiment` the columns from
 #'   `rowData(query)` (rowData(`target`)) are extracted; when *query* (*target*)
-#'   is a [QFeatures()] the columns from `rowData` of the assay specified in the
-#'   `queryAssay` (`targetAssay`) slot are extracted. The matching scores
+#'   is a [QFeatures::QFeatures()] the columns from `rowData` of the assay
+#'   specified in the `queryAssay` (`targetAssay`) slot are extracted.
+#'   The matching scores
 #'   are available as *variable* `"score"`. Similar to a left join between the
 #'   query and target elements, this function returns a value for each query
 #'   element, with eventual duplicated values for query elements matching more
@@ -315,7 +317,7 @@
 #'
 #' @return See individual method description above for details.
 #'
-#' @seealso [MatchedSpectra()] for matched [Spectra()] objects.
+#' @seealso [MatchedSpectra()] for matched [Spectra::Spectra()] objects.
 #'
 #' @exportClass Matched
 #'
@@ -1064,17 +1066,17 @@ pruneTarget <- function(object) {
              call. = FALSE)
     if (length(dim(query)) == 2) {
         if (length(queryColname) == 0)
-            stop("\"", queryColname,
-                 "\" must be set when 'query' is 2-dimensional", call. = FALSE)
+            stop("'queryColname' must be provided when ",
+                 "'query' is 2-dimensional", call. = FALSE)
         if (!queryColname %in% colnames(query))
             stop("\"", queryColname, "\" is not a column of 'query'",
                  call. = FALSE)
     }
     targetColname <- sub("target_", "", targetColname)
     if (length(dim(target)) == 2) {
         if (length(targetColname) == 0)
-            stop("\"", targetColname,
-                 "\" must be set when 'target' is 2-dimensional", call. = FALSE)
+            stop("'targetColname' must be provided when ",
+                 "'target' is 2-dimensional", call. = FALSE)
         if (!targetColname %in% colnames(target))
             stop("\"", targetColname, "\" is not a column of 'target'",
                  call. = FALSE)
@@ -1357,7 +1359,7 @@ setMethod(
                         targetColname = character(),
                         score = rep(NA_real_, length(queryValue)),
                         isIndex = FALSE) {
-    if (!is.data.frame(score))
+    if (is.numeric(score))
         score <- data.frame(score = score)
     if (!is.data.frame(score))
         stop("'score' needs to be either a 'data.frame' or a numeric",
@@ -1374,7 +1376,7 @@ setMethod(
             stop("Provided indices in 'queryValue' are out-of-bounds.",
                  call. = FALSE)
         if (any(!targetValue %in% seq_len(.nelements(target))))
-            stop("Provided indices in 'queryValue' are out-of-bounds.",
+            stop("Provided indices in 'targetValue' are out-of-bounds.",
                  call. = FALSE)
         query_idx <- queryValue
         target_idx <- targetValue
@@ -1432,7 +1434,7 @@ setMethod("addMatches", "Matched",
 #'
 #' @export
 setMethod("endoapply", "ANY", function(X, FUN, ...) {
-    endoapply(X, FUN, ...)
+    S4Vectors::endoapply(X, FUN, ...)
 })
 
 #' @rdname Matched

R/MatchedSpectra.R

@@ -91,7 +91,7 @@
 #'
 #' - `addProcessing`: add a processing step to both the *query* and *target*
 #'   `Spectra` in `object`. Additional parameters for `FUN` can be passed *via*
-#'   `...`. See `addProcessing` documentation in [Spectra()] for more
+#'   `...`. See `addProcessing` documentation in [Spectra::Spectra()] for more
 #'   information.
 #'
 #' - `plotSpectraMirror`: creates a mirror plot between the query and each
@@ -102,18 +102,19 @@
 #'   through `...`.
 #'
 #' - `setBackend`: allows to change the *backend* of both the query and target
-#'   [Spectra()] object. The function will return a `MatchedSpectra` object with
-#'   the query and target `Spectra` changed to the specified `backend`, which
-#'   can be any backend extending [MsBackend].
+#'   [Spectra::Spectra()] object. The function will return a `MatchedSpectra`
+#'   object with the query and target `Spectra` changed to the specified
+#'   `backend`, which can be any backend extending [Spectra::MsBackend].
 #'
-#' @param backend for `setBackend`: instance of an object extending [MsBackend].
-#'   See help for `setBackend` in [Spectra()] for more details.
+#' @param backend for `setBackend`: instance of an object extending
+#'   [Spectra::MsBackend]. See help for [Spectra::setBackend()]
+#'   for more details.
 #'
 #' @param columns for `spectraData`: `character` vector with spectra variable
 #'   names that should be extracted.
 #'
 #' @param FUN for `addProcessing`: function to be applied to the peak matrix
-#'   of each spectrum in `object`. See [Spectra()] for more details.
+#'   of each spectrum in `object`. See [Spectra::Spectra()] for more details.
 #'
 #' @param main for `plotSpectraMirror`: an optional title for each plot.
 #'
@@ -131,7 +132,7 @@
 #'
 #' @param spectraVariables for `addProcessing`: `character` with additional
 #'   spectra variables that should be passed along to the function defined
-#'   with `FUN`. See [Spectra()] for details.
+#'   with `FUN`. See [Spectra::Spectra()] for details.
 #'
 #' @param target `Spectra` with the spectra against which `query` has been
 #'   matched.