Get minfi ready for the switch to virtual DataFrame

- The switch to virtual DataFrame will happen soon in the S4Vectors package.
- Also replace all use of colGrid() with colAutoGrid() (the former is now
  defunct in the DelayedArray package).

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.41.0
+Version: 1.41.1
 Title: Analyze Illumina Infinium DNA methylation arrays
 Description: Tools to analyze & visualize Illumina Infinium methylation arrays.
 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),

R/IlluminaMethylationAnnotation-class.R

@@ -194,7 +194,7 @@ getAnnotation <- function(object, what = "everything", lociNames = NULL,
     # what <- bestOrder[bestOrder %in% what]
 
     out <- do.call(cbind, lapply(what, function(wh) {
-        .annoGet(wh, envir = annoObject@data)
+        updateObject(.annoGet(wh, envir = annoObject@data))
     }))
 
     if (!is.null(lociNames)) {

R/IlluminaMethylationManifest-class.R

@@ -174,18 +174,18 @@ setMethod(
 
 # Exported functions -----------------------------------------------------------
 
-IlluminaMethylationManifest <- function(TypeI = new("DataFrame"),
-                                        TypeII = new("DataFrame"),
-                                        TypeControl = new("DataFrame"),
-                                        TypeSnpI = new("DataFrame"),
-                                        TypeSnpII = new("DataFrame"),
+IlluminaMethylationManifest <- function(TypeI = DataFrame(),
+                                        TypeII = DataFrame(),
+                                        TypeControl = DataFrame(),
+                                        TypeSnpI = DataFrame(),
+                                        TypeSnpII = DataFrame(),
                                         annotation = "") {
     data <- new.env(parent = emptyenv())
-    data[["TypeI"]] <- TypeI
-    data[["TypeII"]] <- TypeII
-    data[["TypeControl"]] <- TypeControl
-    data[["TypeSnpI"]] <- TypeSnpI
-    data[["TypeSnpII"]] <- TypeSnpII
+    data[["TypeI"]] <- updateObject(TypeI)
+    data[["TypeII"]] <- updateObject(TypeII)
+    data[["TypeControl"]] <- updateObject(TypeControl)
+    data[["TypeSnpI"]] <- updateObject(TypeSnpI)
+    data[["TypeSnpII"]] <- updateObject(TypeSnpII)
     lockEnvironment(data, bindings = TRUE)
     new("IlluminaMethylationManifest",
         annotation = annotation,
@@ -221,7 +221,7 @@ getProbeInfo <- function(object,
     if (.isMethylOrRatio(object)) {
         out <- out[out$Name %in% rownames(object),]
     }
-    out
+    updateObject(out)
 }
 
 getManifestInfo <- function(object, type = c("nLoci", "locusNames")) {
@@ -256,6 +256,7 @@ getControlAddress <- function(object,
 
 setMethod("show", "IlluminaMethylationManifest", function(object) {
     cat("IlluminaMethylationManifest object\n")
+    object <- updateObject(object)
     .show.annotation(object@annotation)
     cat("Number of type I probes:", nrow(object@data[["TypeI"]]), "\n")
     cat("Number of type II probes:", nrow(object@data[["TypeII"]]), "\n")

R/MethylSet-class.R

@@ -149,6 +149,8 @@ setMethod(
                     getObjectSlots(object)[["phenoData"]])[["data"]],
                 annotation = getObjectSlots(object)[["annotation"]],
                 preprocessMethod = getObjectSlots(object)[["preprocessMethod"]])
+        } else {
+            object <- callNextMethod()
         }
         object
     }

R/RGChannelSet-class.R

@@ -49,7 +49,7 @@ setMethod(
 
         # Set up ArrayGrid instances over `x` as well as "parallel" ArrayGrid
         # instance over `sink`.
-        x_grid <- colGrid(x)
+        x_grid <- colAutoGrid(x)
         sink_grid <- RegularArrayGrid(
             refdim = dim(sink),
             spacings = c(nrow(sink), ncol(sink) / length(x_grid)))
@@ -214,6 +214,8 @@ setMethod(
                 colData = getObjectSlots(
                     getObjectSlots(object)[["phenoData"]])[["data"]],
                 annotation = getObjectSlots(object)[["annotation"]])
+        } else {
+            object <- callNextMethod()
         }
         object
     }

R/blocks.R

@@ -180,7 +180,7 @@ setMethod(
 
         # Set up ArrayGrid instances over `x` as well as "parallel" ArrayGrid
         # instance over `sink`
-        x_grid <- colGrid(x)
+        x_grid <- colAutoGrid(x)
         sink_grid <- RegularArrayGrid(
             refdim = dim(sink),
             spacings = c(nrow(sink), ncol(sink) / length(x_grid)))

R/detectionP.R

@@ -78,8 +78,8 @@ setMethod(
 
         # Set up ArrayGrid instances over `Red` and `Green` as well as
         # "parallel" ArrayGrid instance over `detP_sink`.
-        Red_grid <- colGrid(Red)
-        Green_grid <- colGrid(Green)
+        Red_grid <- colAutoGrid(Red)
+        Green_grid <- colAutoGrid(Green)
         detP_sink_grid <- RegularArrayGrid(
             refdim = dim(detP_sink),
             spacings = c(nrow(detP_sink), ncol(detP_sink) / length(Red_grid)))

R/preprocessNoob.R

@@ -275,8 +275,8 @@ setMethod(
         # `U_sink`. Also set up "parallel" ArrayGrid instances over `GreenOOB`
         # and `RedOOB`, as well as `Red` and `Green` if performing dye
         # correction.
-        Meth_grid <- colGrid(Meth)
-        Unmeth_grid <- colGrid(Unmeth)
+        Meth_grid <- colAutoGrid(Meth)
+        Unmeth_grid <- colAutoGrid(Unmeth)
         M_sink_grid <- RegularArrayGrid(
             refdim = dim(M_sink),
             spacings = c(nrow(M_sink), ncol(M_sink) / length(Meth_grid)))

R/preprocessRaw.R

@@ -102,8 +102,8 @@ setMethod(
 
         # Set up ArrayGrid instances over `Red` and `Green` as well as
         # "parallel" ArrayGrid instances over `M_sink` and `U_sink`.
-        Red_grid <- colGrid(Red)
-        Green_grid <- colGrid(Green)
+        Red_grid <- colAutoGrid(Red)
+        Green_grid <- colAutoGrid(Green)
         M_sink_grid <- RegularArrayGrid(
             refdim = dim(M_sink),
             spacings = c(nrow(M_sink), Red_grid@spacings[2]))

R/preprocessSwan.R

@@ -148,7 +148,7 @@ setMethod(
 
         # Set up ArrayGrid instances over `x` as well as "parallel" ArrayGrid
         # instances over `bg` and `sink`.
-        x_grid <- colGrid(x)
+        x_grid <- colAutoGrid(x)
         bg_grid <- RegularArrayGrid(
             refdim = dim(bg),
             spacings = c(nrow(bg), ncol(bg) / length(x_grid)))

man/IlluminaMethylationManifest-class.Rd

@@ -22,11 +22,11 @@
 \usage{
 ## Constructor
 
-IlluminaMethylationManifest(TypeI = new("DataFrame"),
-                            TypeII = new("DataFrame"),
-                            TypeControl = new("DataFrame"),
-                            TypeSnpI = new("DataFrame"),
-                            TypeSnpII = new("DataFrame"),
+IlluminaMethylationManifest(TypeI = DataFrame(),
+                            TypeII = DataFrame(),
+                            TypeControl = DataFrame(),
+                            TypeSnpI = DataFrame(),
+                            TypeSnpII = DataFrame(),
                             annotation = "")
 
 ## Data extraction