Merge pull request #1122 from jiajic/suite_dev

docs: Add instructions for adding new methods and operations

R/normalize.R

@@ -1,3 +1,20 @@
+# Data Processing and Pipelining ------------------------------------------ #
+# ADDING NEW METHODS
+# - 1. Define the operation as a function. 
+#      (See # internals / implementations section below)
+#   ## if adding a new operation type ##
+#   - 1.1  Define an extending param class
+#   - 1.2 Create an internal function to generate the class with default params 
+#         (See # internals / params setup)
+#   - 1.3 Update the relevant factory function (normParam, scaleParam, 
+#         adjustParam). Add method to to the `match.arg` and register it in the
+#         switch statement, pointing at the new default params internal 
+#         function.
+# - 2. Add the S4 method for the matrix/param combination desired
+# - 3. Update the method documentation (if a method was added). Both the
+#      operation-specific documentation and under `process_param`, linking
+#      to it.
+
 # Documentation ####
 
 #' @name processExpression

R/zzz.R

@@ -69,11 +69,11 @@
 
         if (requireNamespace("dbMatrix", quietly = TRUE)) {
             setMethod("processData",
-                      signature(x = "dbMatrix", param = "logNormParam"),
-                      function(x, param) {
-                          x[] <- dplyr::mutate(x[], x = x + param$offset)
-                          log(x) / log(param$base)
-                      }
+                signature(x = "dbMatrix", param = "logNormParam"),
+                function(x, param) {
+                    x[] <- dplyr::mutate(x[], x = x + param$offset)
+                    log(x) / log(param$base)
+                }
             )
         }
     })