update documentation

DESCRIPTION

@@ -17,15 +17,18 @@ Authors@R: c(
            email="[email protected]")
         )
 Description: A package to merge, filter sort, organise and otherwise mash 
-    together metabolite annotations. Metabolite annotations can be imported from
-    multiple sources (software) and combined using workflow steps based on S4
-    class templates derived from the `struct` package.
+    together metabolite annotation tables. Metabolite annotations can be 
+    imported from multiple sources (software) and combined using workflow 
+    steps based on S4
+    class templates derived from the `struct` package. Other modular workflow
+    such as filtering, merging, splitting, normalisation and rest-api queries
+    are also included.
 License: GPL-3
 Encoding: UTF-8
 LazyData: false
 RoxygenNote: 7.3.1
 Depends: 
-    R (>= 4.3.0),
+    R (>= 4.4.0),
     struct
 Imports: 
     dplyr,
@@ -37,7 +40,8 @@ Imports:
     ggthemes,
     cowplot,
     ggplot2,
-    utils
+    utils,
+    rlang
 Collate: 
     'generics.R'
     'zzz.R'
@@ -140,5 +144,5 @@ Config/testthat/edition: 3
 VignetteBuilder: knitr
 URL: https://computational-metabolomics.github.io/MetMashR/
 Roxygen: list(markdown = TRUE)
-biocViews: WorkflowStep, Metabolomics
+biocViews: WorkflowStep, Metabolomics, KEGG
 BugReports: https://github.com/computational-metabolomics/MetMashR/issues

NAMESPACE

@@ -97,6 +97,7 @@ import(dplyr, except = as_data_frame)
 import(ggplot2)
 import(ggthemes)
 import(httr)
+import(methods)
 import(rlang)
 importFrom(scales,manual_pal)
 importFrom(utils,capture.output)

R/AnnotationDb_database.R

@@ -3,67 +3,65 @@
 #' @include annotation_database_class.R
 #' @family {annotation databases}
 #' @seealso [AnnotationDbi::AnnotationDb]
-AnnotationDb_database = function(
-        source,
-        table,
-        ...) {
-
+AnnotationDb_database <- function(source,
+                                  table,
+                                  ...) {
     # new object
-    out = struct::new_struct(
-        'AnnotationDb_database',
+    out <- struct::new_struct(
+        "AnnotationDb_database",
         source = source,
         table = table,
         ...
     )
     return(out)
 }
 
-.AnnotationDb_database<-setClass(
+.AnnotationDb_database <- setClass(
     "AnnotationDb_database",
-    contains = 'annotation_database',
+    contains = "annotation_database",
     slots = c(
-        table = 'entity'
+        table = "entity"
     ),
     prototype = list(
-        name = 'AnnotationDb database', 
+        name = "AnnotationDb database",
         description = paste0(
-            'Retrieve a table from an AnnotationDb package.'), 
-        type='AnnotationDb_database',
+            "Retrieve a table from an AnnotationDb package."
+        ),
+        type = "AnnotationDb_database",
         .writable = FALSE,
-        libraries = 'AnnotationDbi',
+        libraries = "AnnotationDbi",
         table = entity(
-            name = 'Table name',
+            name = "Table name",
             description = paste0(
-                'The name of a table to import from the specified source ',
-                'AnnotationDb package.'),
-            type = 'character',
+                "The name of a table to import from the specified source ",
+                "AnnotationDb package."
+            ),
+            type = "character",
             max_length = 1
         ),
         source = entity(
-            name = 'AnnotationDb package name',
+            name = "AnnotationDb package name",
             description = paste0(
-                'The name of an AnnotationDb package to import the specified ',
-                'table from. Note the package should already be installed.'),
-            type = 'character',
+                "The name of an AnnotationDb package to import the specified ",
+                "table from. Note the package should already be installed."
+            ),
+            type = "character",
             max_length = 1
         ),
-        .params = 'table'
+        .params = "table"
     )
 )
 
 #' @export
-setMethod(f="read_database",
-          signature=c("AnnotationDb_database"),definition = function(obj) {
-              
-              # get resource
-              IN = get(obj$table, envir = loadNamespace(obj$source))
-              IN = as.list(IN)
-              IN = stack(IN)
-              colnames(IN)[1] = obj$source
-              # return
-              return(IN[,c(2,1)])
-          }
+setMethod(
+    f = "read_database",
+    signature = c("AnnotationDb_database"), definition = function(obj) {
+        # get resource
+        IN <- get(obj$table, envir = loadNamespace(obj$source))
+        IN <- as.list(IN)
+        IN <- stack(IN)
+        colnames(IN)[1] <- obj$source
+        # return
+        return(IN[, c(2, 1)])
+    }
 )
-
-
-