Changed manifest and annotation constructors

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/minfi@68830 bc3139a8-67e5-0310-9ffc-ced21a209358

Author: khansen

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.3.3
+Version: 1.3.4
 Title: Analyze Illumina's 450k methylation arrays
 Description: Tools for analyzing and visualizing Illumina's 450k array data
 Author: Kasper Daniel Hansen, Martin Aryee

NAMESPACE

@@ -8,7 +8,6 @@ importClassesFrom(Biobase, aggregator, container, eSet,
                   Versions, VersionsNull, Versioned, VersionedBiobase,
                   ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric,
                   ScalarCharacter)
-
 importMethodsFrom(Biobase, "[", "[[", "$", abstract, aggenv, aggfun,
                   annotatedDataFrameFrom, annotation,
                   channel, channelNames, coerce,
@@ -42,7 +41,6 @@ import(GenomicRanges)
 importFrom(Biobase, assayDataElementNames,
            assayDataElement, assayDataElementReplace, "assayDataElement<-",
            "cache", "copyEnv", "copySubstitute")
-
 importFrom(reshape, melt) 
 importFrom(mclust, Mclust)
 importFrom(RColorBrewer, brewer.pal)
@@ -53,9 +51,10 @@ importFrom(limma, squeezeVar, lmFit, eBayes, contrasts.fit)
 importFrom(preprocessCore, normalize.quantiles)
 importFrom(crlmm, readIDAT)
 
-export(manifestNew, getManifest, getProbeData, getProbeInfo, getManifestInfo,
+export(getManifest, getProbeData, getProbeInfo, getManifestInfo,
        getControlAddress, getRed, getGreen, getMeth, getUnmeth,
        getBeta, getM, dmpFinder, mdsPlot, plotCpg, preprocessRaw,
+       IlluminaMethylationManifest, IlluminaMethylationAnnotation,
        normalize.illumina.control, bgcorrect.illumina, preprocessIllumina,
        preprocessSWAN, plotBetasByType,
        detectionP, qcReport, controlStripPlot, densityBeanPlot, densityPlot,

R/class.R

@@ -152,7 +152,7 @@ setMethod("show", "IlluminaMethylationManifest", function(object) {
     cat("Number of control probes:", nrow(object@data[["TypeControl"]]), "\n")
 })
 
-manifestNew <- function(TypeI = new("data.frame"), TypeII = new("data.frame"),
+IlluminaMethylationManifest <- function(TypeI = new("data.frame"), TypeII = new("data.frame"),
                         TypeControl = new("data.frame"), annotation = "") {
     data <- new.env(parent = emptyenv())
     data[["TypeI"]] <- TypeI
@@ -163,7 +163,6 @@ manifestNew <- function(TypeI = new("data.frame"), TypeII = new("data.frame"),
     manifest
 }
 
-
 setClass("IlluminaMethylationAnnotation",
          representation(data = "environment",
                         annotation = "character"))
@@ -178,3 +177,17 @@ setMethod("show", "IlluminaMethylationAnnotation", function(object) {
     cat("Annotation:", object@annotation, "\n")
 })
 
+IlluminaMethylationAnnotation <- function(listOfObjects,
+                                          annotation = "") {
+    data <- new.env(parent = emptyenv())
+    stopifnot(all(c("Locations.hg18", "Locations.hg19") %in% names(listOfObjects)))
+    for(nam in names(listOfObjects)) {
+        cat(nam, "\n")
+        assign(nam, listOfObjects[[nam]], envir = data)
+    }
+    lockEnvironment(data, bindings = TRUE)
+    anno <- new("IlluminaMethylationAnnotation",
+                annotation = annotation, data = data)
+    anno
+}
+

man/IlluminaMethylationAnnotation-class.Rd

@@ -2,6 +2,7 @@
 \Rdversion{1.1}
 \docType{class}
 \alias{IlluminaMethylationAnnotation-class}
+\alias{IlluminaMethylationAnnotation}
 \alias{show,IlluminaMethylationAnnotation-method}
 \title{Class \code{"IlluminaMethylationAnnotation"}}
 \description{
@@ -12,7 +13,8 @@
 }
 \section{Objects from the Class}{
 Objects can be created by calls of the form
-\code{new("IlluminaMethylationAnnotation", ...)}.
+\code{new("IlluminaMethylationAnnotation", ...)}, but the preferred way
+is to use \code{IlluminaMethylationAnnotation()}.
 }
 \section{Slots}{
   \describe{

man/IlluminaMethylationManifest-class.Rd

@@ -2,7 +2,7 @@
 \Rdversion{1.1}
 \docType{class}
 \alias{IlluminaMethylationManifest-class}
-\alias{manifestNew}
+\alias{IlluminaMethylationManifest}
 \alias{show,IlluminaMethylationManifest-method}
 \title{Class \code{"IlluminaMethylationManifest"}}
 \description{
@@ -12,7 +12,7 @@
 \section{Objects from the Class}{
 Objects can be created by calls of the form
 \code{new("IlluminaMethylationManifest", ...)}, but the preferred way is
-to use \code{manifestNew()}.
+to use \code{IlluminaMethylationManifest()}.
 }
 \section{Slots}{
   \describe{