From 4055b7f4c1131ea1aecfd22c79b7f12f0b1efecf Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 22 Feb 2017 12:06:28 -0800
Subject: [PATCH 01/12] add noobPipeline(rgSet) function to make my life easier

---
 DESCRIPTION              |  2 +-
 R/preprocessNoob.R       | 10 +++++++
 inst/extData/GM12878.csv | 59 ++++++++++++++++++++++++++++++++++++++++
 man/preprocessNoob.Rd    |  8 +++++-
 4 files changed, 77 insertions(+), 2 deletions(-)
 create mode 100644 inst/extData/GM12878.csv

diff --git a/DESCRIPTION b/DESCRIPTION
index 099c9e4..2f43211 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.21.5
+Version: 1.21.6
 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"),
diff --git a/R/preprocessNoob.R b/R/preprocessNoob.R
index 7d04740..6099044 100644
--- a/R/preprocessNoob.R
+++ b/R/preprocessNoob.R
@@ -204,3 +204,13 @@ normexp.get.xcs <- function(xcf, params){
         xcf[,i] <- normexp.signal(as.numeric((pars[i,])), xcf[,i] ) # from limma
     return( xcf + params[[grep('offset', names(params), value=TRUE)]][1] )
 }
+
+# a "best practices" baseline for reading IDATs
+noobPipeline <- function(rgSet, pCutoff=0.01) {
+  pvals <- detectionP(rgSet)
+  grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
+  is.na(assays(grSet)$Beta) <- pval[rownames(grSet),] >= pCutoff 
+  grSet$predictedSex <- getSex(grSet)$predictedSex
+  metadata(grSet)$SNPs <- getSnpBeta(rgSet)
+  return(grSet)
+}
diff --git a/inst/extData/GM12878.csv b/inst/extData/GM12878.csv
new file mode 100644
index 0000000..08ea5d8
--- /dev/null
+++ b/inst/extData/GM12878.csv
@@ -0,0 +1,59 @@
+"","seqnames","start","end","width","strand","score","genotype","ref","alt","U","M"
+"rs3936238","chr1",4031586,4031586,1,"*",3,"A:A","A","G","G","A"
+"rs877309","chr1",11412265,11412265,1,"*",2,"A:G","A","G","A","G"
+"rs213028","chr1",21524764,21524764,1,"*",2,"C:T","C","T","C","T"
+"rs11249206","chr1",25150569,25150569,1,"*",1,"T:T","C","T","T","C"
+"rs654498","chr1",81945636,81945636,1,"*",1,"C:C","C","T","C","T"
+"rs715359","chr1",175697791,175697791,1,"*",1,"C:C","T","C","C","T"
+"rs2804694","chr1",179598456,179598456,1,"*",1,"A:A","G","A","A","G"
+"rs6426327","chr1",244156434,244156434,1,"*",1,"A:A","G","A","A","G"
+"rs966367","chr2",12065671,12065671,1,"*",3,"C:C","C","T","T","C"
+"rs4331560","chr2",48938177,48938177,1,"*",3,"G:G","A","G","A","G"
+"rs1510480","chr2",60678945,60678945,1,"*",2,"A:G","G","A","A","G"
+"rs6546473","chr2",69113861,69113861,1,"*",1,"A:A","A","G","A","G"
+"rs264581","chr2",159679609,159679609,1,"*",1,"A:A","A","G","A","G"
+"rs939290","chr3",14633870,14633870,1,"*",3,"C:C","T","C","T","C"
+"rs9839873","chr3",86744845,86744845,1,"*",3,"C:C","T","C","T","C"
+"rs1520670","chr3",100455616,100455616,1,"*",3,"A:A","A","G","G","A"
+"rs10936224","chr3",162385225,162385225,1,"*",2,"A:G","G","A",NA,NA
+"rs10033147","chr4",13966228,13966228,1,"*",1,NA,"A","G",NA,NA
+"rs2125573","chr4",128827282,128827282,1,"*",2,"T:C","T","C",NA,NA
+"rs7660805","chr4",131263500,131263500,1,"*",1,"A:A","G","A","A","G"
+"rs9292570","chr5",35036069,35036069,1,"*",3,"C:C","T","C","T","C"
+"rs348937","chr5",112853576,112853576,1,"*",1,"T:T","C","T","T","C"
+"rs1019916","chr5",146628552,146628552,1,"*",2,"G:A","G","A",NA,NA
+"rs7746156","chr6",47238778,47238778,1,"*",2,"C:T","T","C",NA,NA
+"rs9363764","chr6",68288763,68288763,1,"*",2,"G:A","G","A",NA,NA
+"rs10457834","chr6",149084493,149084493,1,"*",3,"C:C","T","C","T","C"
+"rs6982811","chr8",36666471,36666471,1,"*",1,NA,"T","C",NA,NA
+"rs1484127","chr8",51888207,51888207,1,"*",1,"A:A","G","A","A","G"
+"rs6471533","chr8",96539476,96539476,1,"*",2,"G:A","G","A",NA,NA
+"rs472920","chr8",96917920,96917920,1,"*",1,NA,"A","G",NA,NA
+"rs6991394","chr8",121851583,121851583,1,"*",3,NA,"C","T",NA,NA
+"rs2385226","chr8",126751178,126751178,1,"*",2,"T:C","C","T",NA,NA
+"rs4742386","chr9",7701758,7701758,1,"*",1,NA,"A","G",NA,NA
+"rs1040870","chr9",84605357,84605357,1,"*",2,"T:C","C","T",NA,NA
+"rs10796216","chr10",14731895,14731895,1,"*",3,"A:A","A","G","G","A"
+"rs10882854","chr10",98629087,98629087,1,"*",1,"C:C","T","C","C","T"
+"rs11034952","chr11",38745191,38745191,1,"*",2,"C:T","T","C","C","T"
+"rs1945975","chr11",104804934,104804934,1,"*",2,"T:C","C","A","A","C"
+"rs2468330","chr12",41484989,41484989,1,"*",2,"A:G","G","A","A","G"
+"rs1495031","chr12",61784403,61784403,1,"*",2,"T:C","C","T","T","C"
+"rs951295","chr15",43787115,43787115,1,"*",1,"G:G","A","G","G","A"
+"rs2959823","chr15",74200584,74200584,1,"*",2,"A:G","G","A","A","G"
+"rs1510189","chr16",54658025,54658025,1,"*",1,"T:T","T","C","T","C"
+"rs1941955","chr18",33416836,33416836,1,"*",1,"T:T","T","C","T","C"
+"rs2235751","chr20",1917934,1917934,1,"*",2,"A:G","A","G","A","G"
+"rs845016","chr21",32920155,32920155,1,"*",3,"C:C","C","T","T","C"
+"rs2032088","chr21",37399200,37399200,1,"*",1,"A:A","G","A","A","G"
+"rs1467387","chr22",24261372,24261372,1,"*",2,"T:C","T","C","T","C"
+"rs133860","chr22",24474760,24474760,1,"*",2,"T:C","C","T","T","C"
+"rs739259","chr22",25686579,25686579,1,"*",2,"A:G","A","G","A","G"
+"rs2857639","chr22",28385674,28385674,1,"*",2,"A:G","A","G","A","G"
+"rs2208123","chr22",46593476,46593476,1,"*",3,"A:A","A","G","G","A"
+"rs2521373","chrX",9436990,9436990,1,"*",2,"A:G","A","G",NA,NA
+"rs798149","chrX",15795352,15795352,1,"*",3,"G:G","A","G","A","G"
+"rs5926356","chrX",28157252,28157252,1,"*",2,"A:G","A","G",NA,NA
+"rs5987737","chrX",114616977,114616977,1,"*",1,NA,"T","C",NA,NA
+"rs1416770","chrX",145026857,145026857,1,"*",2,"T:C","T","C",NA,NA
+"rs6626309","chrX",147012065,147012065,1,"*",3,NA,"C","T",NA,NA
diff --git a/man/preprocessNoob.Rd b/man/preprocessNoob.Rd
index 79c5855..d3d76b2 100644
--- a/man/preprocessNoob.Rd
+++ b/man/preprocessNoob.Rd
@@ -1,5 +1,6 @@
 \name{preprocessNoob}
 \alias{preprocessNoob}
+\alias{noobPipeline}
 \title{
   The Noob/ssNoob preprocessing method for Infinium methylation microarrays.
 }
@@ -10,6 +11,8 @@
 \usage{
 preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = TRUE,
                dyeMethod=c("single", "reference"))
+
+noobPipeline(rgSet, pCutoff = 0.01)
 }
 \arguments{
   \item{rgSet}{An object of class \code{RGChannelSet}.}
@@ -17,9 +20,11 @@ preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = TRUE,
   \item{dyeCorr}{Should dye correction be done?}
   \item{verbose}{Should the function be verbose?}
   \item{dyeMethod}{How should dye bias correction be done: use a single sample approach (ssNoob), or a reference array?}
+  \item{pCutoff}{(for noobPipeline) Above what detection pvalue should probes be marked NA? (0.01)}
 }
 \value{
-  An object of class \code{MethylSet}.
+  For preprocessNoob, an object of class \code{MethylSet}.
+  For noobPipeline, an object of class \code{GenomicRatioSet} with SNP metadata.
 }
 \references{
   TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund
@@ -42,6 +47,7 @@ if (require(minfiData)) {
   ## RGsetEx.sub is a small subset of RGsetEx; 
   ## only used for computational speed.
   MsetEx.sub.noob <- preprocessNoob(RGsetEx.sub)
+  grSet.sub.noob <- noobPipeline(RGsetEx.sub)
 }
 \dontrun{
 if (require(minfiData)) {

From a6f96a5818668a63639f05fe2843ac578f8dd8e9 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 22 Feb 2017 12:15:35 -0800
Subject: [PATCH 02/12] fix NAMESPACE to export noobPipeline()

---
 NAMESPACE          | 2 +-
 R/preprocessNoob.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 8b7ee4f..6b3b9ca 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -57,7 +57,7 @@ export(getManifest, getProbeInfo, getManifestInfo,
        normalize.illumina.control, bgcorrect.illumina,
        preprocessRaw, preprocessIllumina,
        preprocessSWAN, preprocessQuantile,
-       preprocessFunnorm, preprocessNoob,
+       preprocessFunnorm, preprocessNoob, noobPipeline,
        RGChannelSet, RGChannelSetExtended,
        MethylSet, RatioSet,
        GenomicMethylSet, GenomicRatioSet,
diff --git a/R/preprocessNoob.R b/R/preprocessNoob.R
index 6099044..d04289e 100644
--- a/R/preprocessNoob.R
+++ b/R/preprocessNoob.R
@@ -207,7 +207,7 @@ normexp.get.xcs <- function(xcf, params){
 
 # a "best practices" baseline for reading IDATs
 noobPipeline <- function(rgSet, pCutoff=0.01) {
-  pvals <- detectionP(rgSet)
+  pval <- detectionP(rgSet)
   grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
   is.na(assays(grSet)$Beta) <- pval[rownames(grSet),] >= pCutoff 
   grSet$predictedSex <- getSex(grSet)$predictedSex

From 7d9d63015ba8eafb6bd0a413c1337b1d935d8b95 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 22 Feb 2017 12:17:19 -0800
Subject: [PATCH 03/12] don't try predicting sex, as it can fail

---
 R/preprocessNoob.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/preprocessNoob.R b/R/preprocessNoob.R
index d04289e..ff6c66d 100644
--- a/R/preprocessNoob.R
+++ b/R/preprocessNoob.R
@@ -210,7 +210,6 @@ noobPipeline <- function(rgSet, pCutoff=0.01) {
   pval <- detectionP(rgSet)
   grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
   is.na(assays(grSet)$Beta) <- pval[rownames(grSet),] >= pCutoff 
-  grSet$predictedSex <- getSex(grSet)$predictedSex
   metadata(grSet)$SNPs <- getSnpBeta(rgSet)
   return(grSet)
 }

From 1ac7121754f0e8e514467d240e4adb1a822a4ffb Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Sun, 9 Apr 2017 11:10:35 -0700
Subject: [PATCH 04/12] adding some rudimentary support for SNP tracking

---
 DESCRIPTION  |  9 +++++----
 R/generics.R |  1 +
 R/grset.R    | 17 +++++++++++++++++
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2f43211..a16e032 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.21.6
+Version: 1.21.7
 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"),
@@ -12,7 +12,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
              person("Jean-Philippe", "Fortin", role = "ctb"),
              person("Tim", "Triche", role = "ctb"),
              person(c("Shan", "V."), "Andrews", role = "ctb"))
-Depends:  methods,
+Depends: methods,
 	  BiocGenerics (>= 0.15.3),
 	  GenomicRanges,
 	  SummarizedExperiment (>= 1.1.6),
@@ -28,7 +28,7 @@ Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0),
 	  BiocStyle,
 	  knitr,
 	  rmarkdown
-Imports:  S4Vectors,
+Imports: S4Vectors,
 	  GenomeInfoDb,
 	  Biobase (>= 2.33.2),
 	  IRanges,
@@ -53,7 +53,7 @@ Imports:  S4Vectors,
           grDevices,
           graphics,
           utils
-Collate:  generics.R
+Collate: generics.R
 	  mset.R
 	  rset.R
 	  rgset.R
@@ -91,3 +91,4 @@ BugReports: https://github.com/kasperdanielhansen/minfi/issues
 LazyData: yes
 biocViews: DNAMethylation, DifferentialMethylation, Epigenetics, Microarray, MethylationArray,
 	   MultiChannel, TwoChannel, DataImport, Normalization, Preprocessing, QualityControl
+RoxygenNote: 6.0.1
diff --git a/R/generics.R b/R/generics.R
index db4aa47..f1004d5 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -8,5 +8,6 @@ setGeneric("getManifest", function(object) standardGeneric("getManifest"))
 ## setGeneric("getLocations", function(object, ...) standardGeneric("getLocations"))
 setGeneric("preprocessMethod", function(object) standardGeneric("preprocessMethod"))
 setGeneric("getCN", function(object, ...) standardGeneric("getCN"))
+setGeneric("getSNPs", function(object) standardGeneric("getSNPs"))
 setGeneric("convertArray", function(object, ...) standardGeneric("convertArray"))
 setGeneric("combineArrays", function(object1, object2, ...) standardGeneric("combineArrays"))
diff --git a/R/grset.R b/R/grset.R
index 66797a8..756a4b9 100644
--- a/R/grset.R
+++ b/R/grset.R
@@ -70,6 +70,23 @@ setMethod("getCN", signature(object = "GenomicRatioSet"),
               return(NULL)
           })
 
+# FIXME: enforce something a bit less lackadaisical?
+setMethod("getSNPs", signature(object = "GenomicRatioSet"),
+          function (object) {
+              if (!all(colnames(object) %in% colnames(metadata(object)$SNPs))) {
+                missed <- setdiff(colnames(object), 
+                                  colnames(metadata(object)$SNPs))
+                stop("Error: columns for ", paste(missed, sep=", "),
+                     " are missing from metadata(object)$SNPs.")
+              }
+              if ("SNPs" %in% names(metadata(object))) { 
+                return(metadata(object)$SNPs[, colnames(object)])
+              } else {
+                message("No SNPs found in your GenomicRatioSet's metadata.")
+                return(NULL)
+              }
+          })
+
 setMethod("mapToGenome", signature(object = "GenomicRatioSet"),
           function(object, ...) {
               object

From f8a56b4d8556e5c359a452e304ec7ba44addf6b9 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Mon, 10 Apr 2017 13:39:33 -0700
Subject: [PATCH 05/12] Check to see if colnames(SNPs) == colnames(grset), else
 warn

---
 R/grset.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/grset.R b/R/grset.R
index 756a4b9..a3e2a4d 100644
--- a/R/grset.R
+++ b/R/grset.R
@@ -79,10 +79,15 @@ setMethod("getSNPs", signature(object = "GenomicRatioSet"),
                 stop("Error: columns for ", paste(missed, sep=", "),
                      " are missing from metadata(object)$SNPs.")
               }
-              if ("SNPs" %in% names(metadata(object))) { 
+              if ("SNPs" %in% names(metadata(object))) {
+                if (!identical(colnames(object), 
+                               colnames(metadata(object)$SNPs))) {
+                  message("colnames(metadata(object)$SNPs) != colnames(object)")
+                  message("You should probably fix this if you use these SNPs.")
+                }
                 return(metadata(object)$SNPs[, colnames(object)])
               } else {
-                message("No SNPs found in your GenomicRatioSet's metadata.")
+                message("No SNPs found in your GenomicRatioSet metadata().")
                 return(NULL)
               }
           })

From 4509728bc8f25f4fff711df38a9382231eed386e Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Tue, 11 Apr 2017 18:51:12 -0700
Subject: [PATCH 06/12] expose getSNPs() method

---
 NAMESPACE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0f4f51d..b6213ce 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,7 +48,7 @@ export(getManifest, getProbeInfo, getManifestInfo,
        IlluminaMethylationManifest, IlluminaMethylationAnnotation,
        getControlAddress, 
        getRed, getGreen, getNBeads, getMeth, getUnmeth,
-       getBeta, getM, getCN, getMethSignal,
+       getBeta, getM, getCN, getSNPs, getMethSignal,
        getOOB, getSnpBeta,
        dropMethylationLoci, getLocations, getAnnotation,
        getAnnotationObject,

From 09d9f40d00eb2daf92d415972a333c7f8e56a267 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 12 Apr 2017 15:41:55 -0700
Subject: [PATCH 07/12] add getSNPs method for RGChannelSet and export it

---
 NAMESPACE | 5 +++--
 R/rgset.R | 6 ++++++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index b6213ce..d53e137 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -80,8 +80,9 @@ exportClasses(RGChannelSet, RGChannelSetExtended,
               GenomicMethylSet, GenomicRatioSet,
               IlluminaMethylationManifest, IlluminaMethylationAnnotation)
 
-exportMethods(show, initialize, getBeta, getM, getCN, getMeth, getUnmeth,
-              getManifest, annotation, "annotation<-", preprocessMethod,
+exportMethods(show, initialize, 
+              getBeta, getM, getCN, getSNPs, getMeth, getUnmeth, getManifest, 
+              annotation, "annotation<-", preprocessMethod,
               combine, mapToGenome, ratioConvert, bumphunter,
               pData, "pData<-", sampleNames, "sampleNames<-",
               featureNames, "featureNames<-", coerce)
diff --git a/R/rgset.R b/R/rgset.R
index 06d7028..1fa70b1 100644
--- a/R/rgset.R
+++ b/R/rgset.R
@@ -148,6 +148,12 @@ setMethod("getBeta", signature(object = "RGChannelSet"),
               callGeneric(object, ...)
           })
 
+# wrap getSnpBeta function, for RGChannelSet objects 
+setMethod("getSNPs", signature(object = "RGChannelSet"),
+          function (object) {
+              getSnpBeta(object)
+          })
+
 setMethod("mapToGenome", signature(object = "RGChannelSet"),
           function(object, ...) {
               object <- preprocessRaw(object)

From 1a0c58255f10e3935d540fa35e17cd2455cf9cc6 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Sun, 16 Apr 2017 19:35:31 -0700
Subject: [PATCH 08/12] break out noobPipeline into its own function

---
 DESCRIPTION        |  1 +
 R/noobPipeline.R   | 14 ++++++++++++++
 R/preprocessNoob.R |  9 ---------
 3 files changed, 15 insertions(+), 9 deletions(-)
 create mode 100644 R/noobPipeline.R

diff --git a/DESCRIPTION b/DESCRIPTION
index a16e032..caf62e9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -74,6 +74,7 @@ Collate: generics.R
 	  preprocessQuantile.R
 	  preprocessNoob.R
 	  preprocessFunnorm.R
+	  noobPipeline.R
 	  qc.R
 	  read.450k.R
 	  read.meth.R
diff --git a/R/noobPipeline.R b/R/noobPipeline.R
new file mode 100644
index 0000000..7b28e83
--- /dev/null
+++ b/R/noobPipeline.R
@@ -0,0 +1,14 @@
+# a "best practices" baseline for most studies
+noobPipeline <- function(rgSet, pCutoff=0.01) {
+  pval <- detectionP(rgSet)
+  message("Running TCGA-style noob pipeline on ", ncol(rgSet), " samples...")
+  grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
+  message("Masking probes with detection p-value > ", pCutoff, "...")
+  is.na(assays(grSet)$Beta) <- (pval[rownames(grSet),] >= pCutoff)
+  message("Dropping redundant \"M\" assay matrix...")
+  assays(grSet) <- assays(grSet)[c("Beta","CN")]
+  message("Placing SNP probe betas in metadata(grSet)$SNPs...")
+  metadata(grSet)$SNPs <- getSnpBeta(rgSet)
+  message("Done.")
+  return(grSet)
+}
diff --git a/R/preprocessNoob.R b/R/preprocessNoob.R
index ff6c66d..7d04740 100644
--- a/R/preprocessNoob.R
+++ b/R/preprocessNoob.R
@@ -204,12 +204,3 @@ normexp.get.xcs <- function(xcf, params){
         xcf[,i] <- normexp.signal(as.numeric((pars[i,])), xcf[,i] ) # from limma
     return( xcf + params[[grep('offset', names(params), value=TRUE)]][1] )
 }
-
-# a "best practices" baseline for reading IDATs
-noobPipeline <- function(rgSet, pCutoff=0.01) {
-  pval <- detectionP(rgSet)
-  grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
-  is.na(assays(grSet)$Beta) <- pval[rownames(grSet),] >= pCutoff 
-  metadata(grSet)$SNPs <- getSnpBeta(rgSet)
-  return(grSet)
-}

From 142f42ef2688cb7cfb29552a233aa178de10b0d9 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Thu, 20 Apr 2017 12:16:22 -0700
Subject: [PATCH 09/12] add unit tests for noobPipeline and getSNPs

---
 inst/unitTests/test_noobPipeline.R | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 inst/unitTests/test_noobPipeline.R

diff --git a/inst/unitTests/test_noobPipeline.R b/inst/unitTests/test_noobPipeline.R
new file mode 100644
index 0000000..5f18441
--- /dev/null
+++ b/inst/unitTests/test_noobPipeline.R
@@ -0,0 +1,7 @@
+test_noobPipeline <- function() {
+    stopifnot(require(minfiData))
+    grSetEx <- noobPipeline(updateObject(RGsetEx))
+    checkIdentical(getSNPs(grSetEx), getSNPs(updateObject(RGsetEx)))
+    checkIdentical(preprocessMethod(grSetEx), 
+                   c(mu.norm="Noob, dyeCorr=TRUE, dyeMethod=single")) 
+}

From c3f1dca5e2c420164e181e5048b3de59e5243961 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Thu, 20 Apr 2017 12:51:30 -0700
Subject: [PATCH 10/12] add documentation for noobPipeline and default to TCGA
 settings (p>0.05)

---
 R/noobPipeline.R      |  2 +-
 man/noobPipeline.Rd   | 45 +++++++++++++++++++++++++++++++++++++++++++
 man/preprocessNoob.Rd |  2 +-
 3 files changed, 47 insertions(+), 2 deletions(-)
 create mode 100644 man/noobPipeline.Rd

diff --git a/R/noobPipeline.R b/R/noobPipeline.R
index 7b28e83..bf5e357 100644
--- a/R/noobPipeline.R
+++ b/R/noobPipeline.R
@@ -1,5 +1,5 @@
 # a "best practices" baseline for most studies
-noobPipeline <- function(rgSet, pCutoff=0.01) {
+noobPipeline <- function(rgSet, pCutoff=0.05) {
   pval <- detectionP(rgSet)
   message("Running TCGA-style noob pipeline on ", ncol(rgSet), " samples...")
   grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
diff --git a/man/noobPipeline.Rd b/man/noobPipeline.Rd
new file mode 100644
index 0000000..4553a55
--- /dev/null
+++ b/man/noobPipeline.Rd
@@ -0,0 +1,45 @@
+\name{noobPipeline}
+\alias{noobPipeline}
+\alias{noobPipeline}
+\title{
+  A TCGA-style preprocessing pipeline for Infinium methylation microarrays.
+}
+\description{
+  The standard processing pipeline for the Cancer Genome Atlas (TCGA) was 
+  the methylumi implementation of preprocessNoob (which returns identical beta/M
+  values to the ssNoob implementation now standard in minfi).  Probes with 
+  detection p-values > 0.05 were masked as NA, SNP probes for label swap QC
+  tabulated, and the results uploaded as Level 2 data after certain masking 
+  steps (related to common SNPs and repetitive regions) had been applied.
+  This function wraps the individual steps to turn an \code{RGChannelSet} into 
+  a \code{GenomicRatioSet} directly comparable to canonical TCGA datasets. 
+}
+\usage{
+noobPipeline(rgSet, pCutoff=0.05)
+}
+\arguments{
+  \item{rgSet}{An object of class \code{RGChannelSet}.}
+  \item{pCutoff}{Above what detection pvalue should probes be marked NA? (0.05)}
+}
+\value{
+  An object of class \code{GenomicRatioSet} with additional SNP metadata.
+}
+\references{
+  TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund
+  \emph{Low-level processing of Illumina Infinium DNA Methylation
+    BeadArrays}.
+  Nucleic Acids Res (2013) 41, e90.
+  doi:\href{http://www.dx.doi.org/10.1093/nar/gkt090}{10.1093/nar/gkt090}.
+}
+\author{
+  Tim Triche, Jr.
+}
+\seealso{
+  \code{\linkS4class{RGChannelSet}}
+}
+\examples{
+if (require(minfiData)) {
+  grSetEx <- noobPipeline(RGsetEx)
+  identical(getSNPs(grSetEx), getSNPs(RGsetEx))
+}
+}
diff --git a/man/preprocessNoob.Rd b/man/preprocessNoob.Rd
index d3d76b2..b9f3a82 100644
--- a/man/preprocessNoob.Rd
+++ b/man/preprocessNoob.Rd
@@ -1,6 +1,5 @@
 \name{preprocessNoob}
 \alias{preprocessNoob}
-\alias{noobPipeline}
 \title{
   The Noob/ssNoob preprocessing method for Infinium methylation microarrays.
 }
@@ -41,6 +40,7 @@ noobPipeline(rgSet, pCutoff = 0.01)
   as well as \code{\linkS4class{IlluminaMethylationManifest}} for the
   basic classes involved in these functions.
   \code{\link{preprocessRaw}} and \code{\link{preprocessQuantile}} are other preprocessing functions.
+  \code{\link{noobPipeline}} for an end-to-end processing pipeline with results directly comparable to the Cancer Genome Atlas (TCGA) DNA methylation data. 
 }
 \examples{
 if (require(minfiData)) {

From 8b0a033b8d5bbeec5808c7f5b31de059517bec31 Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 10 May 2017 15:10:23 -0700
Subject: [PATCH 11/12] tidying up per Kasper; hello, tcgaPipeline()

---
 DESCRIPTION                          |  4 +--
 NAMESPACE                            |  6 ++--
 R/generics.R                         |  2 +-
 R/grset.R                            |  2 +-
 R/rgset.R                            | 49 +++++++++++++------------
 R/{noobPipeline.R => tcgaPipeline.R} |  8 ++---
 inst/unitTests/test_noobPipeline.R   |  7 ----
 inst/unitTests/test_tcgaPipeline.R   |  7 ++++
 man/noobPipeline.Rd                  | 45 -----------------------
 man/tcgaPipeline.Rd                  | 53 ++++++++++++++++++++++++++++
 10 files changed, 94 insertions(+), 89 deletions(-)
 rename R/{noobPipeline.R => tcgaPipeline.R} (55%)
 delete mode 100644 inst/unitTests/test_noobPipeline.R
 create mode 100644 inst/unitTests/test_tcgaPipeline.R
 delete mode 100644 man/noobPipeline.Rd
 create mode 100644 man/tcgaPipeline.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index cb81a6f..7e3390b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.23.2
+Version: 1.23.3
 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"),
@@ -74,7 +74,7 @@ Collate: generics.R
 	  preprocessQuantile.R
 	  preprocessNoob.R
 	  preprocessFunnorm.R
-	  noobPipeline.R
+	  tcgaPipeline.R
 	  qc.R
 	  read.450k.R
 	  read.meth.R
diff --git a/NAMESPACE b/NAMESPACE
index d53e137..9467074 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,7 +48,7 @@ export(getManifest, getProbeInfo, getManifestInfo,
        IlluminaMethylationManifest, IlluminaMethylationAnnotation,
        getControlAddress, 
        getRed, getGreen, getNBeads, getMeth, getUnmeth,
-       getBeta, getM, getCN, getSNPs, getMethSignal,
+       getBeta, getM, getCN, getSnpBeta, getMethSignal,
        getOOB, getSnpBeta,
        dropMethylationLoci, getLocations, getAnnotation,
        getAnnotationObject,
@@ -57,7 +57,7 @@ export(getManifest, getProbeInfo, getManifestInfo,
        normalize.illumina.control, bgcorrect.illumina,
        preprocessRaw, preprocessIllumina,
        preprocessSWAN, preprocessQuantile,
-       preprocessFunnorm, preprocessNoob, noobPipeline,
+       preprocessFunnorm, preprocessNoob, tcgaPipeline,
        RGChannelSet, RGChannelSetExtended,
        MethylSet, RatioSet,
        GenomicMethylSet, GenomicRatioSet,
@@ -81,7 +81,7 @@ exportClasses(RGChannelSet, RGChannelSetExtended,
               IlluminaMethylationManifest, IlluminaMethylationAnnotation)
 
 exportMethods(show, initialize, 
-              getBeta, getM, getCN, getSNPs, getMeth, getUnmeth, getManifest, 
+              getBeta, getM, getCN, getSnpBeta, getMeth, getUnmeth, getManifest,
               annotation, "annotation<-", preprocessMethod,
               combine, mapToGenome, ratioConvert, bumphunter,
               pData, "pData<-", sampleNames, "sampleNames<-",
diff --git a/R/generics.R b/R/generics.R
index f1004d5..611457e 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -8,6 +8,6 @@ setGeneric("getManifest", function(object) standardGeneric("getManifest"))
 ## setGeneric("getLocations", function(object, ...) standardGeneric("getLocations"))
 setGeneric("preprocessMethod", function(object) standardGeneric("preprocessMethod"))
 setGeneric("getCN", function(object, ...) standardGeneric("getCN"))
-setGeneric("getSNPs", function(object) standardGeneric("getSNPs"))
+setGeneric("getSnpBeta", function(object) standardGeneric("getSnpBeta"))
 setGeneric("convertArray", function(object, ...) standardGeneric("convertArray"))
 setGeneric("combineArrays", function(object1, object2, ...) standardGeneric("combineArrays"))
diff --git a/R/grset.R b/R/grset.R
index a3e2a4d..c297654 100644
--- a/R/grset.R
+++ b/R/grset.R
@@ -71,7 +71,7 @@ setMethod("getCN", signature(object = "GenomicRatioSet"),
           })
 
 # FIXME: enforce something a bit less lackadaisical?
-setMethod("getSNPs", signature(object = "GenomicRatioSet"),
+setMethod("getSnpBeta", signature(object = "GenomicRatioSet"),
           function (object) {
               if (!all(colnames(object) %in% colnames(metadata(object)$SNPs))) {
                 missed <- setdiff(colnames(object), 
diff --git a/R/rgset.R b/R/rgset.R
index 81acd1a..6be1e65 100644
--- a/R/rgset.R
+++ b/R/rgset.R
@@ -112,27 +112,32 @@ getNBeads <- function(object) {
     assay(object, "NBeads")
 }
 
+setMethod("getSnpBeta", signature(object = "RGChannelSet"),
+          function (object) {
 
-getSnpBeta <- function(object){
-    .isRGOrStop(object)
+              .isRGOrStop(object)
 
-    snpProbesII <- getProbeInfo(object, type = "SnpII")$Name
-    M.II <- getGreen(object)[getProbeInfo(object, type = "SnpII")$AddressA,,drop=FALSE]
-    U.II <- getRed(object)[getProbeInfo(object, type = "SnpII")$AddressA,,drop=FALSE]
-
-    snpProbesI.Green <- getProbeInfo(object, type = "SnpI")[getProbeInfo(object, type = "SnpI")$Color=="Grn",,drop=FALSE]
-    snpProbesI.Red <- getProbeInfo(object, type = "SnpI")[getProbeInfo(object, type = "SnpI")$Color=="Red",,drop=FALSE]
-    M.I.Red <- getRed(object)[snpProbesI.Red$AddressB,,drop=FALSE]
-    U.I.Red <- getRed(object)[snpProbesI.Red$AddressA,,drop=FALSE]
-    M.I.Green <- getGreen(object)[snpProbesI.Green$AddressB,,drop=FALSE]
-    U.I.Green <- getGreen(object)[snpProbesI.Green$AddressA,,drop=FALSE]
-    
-    M <- rbind(M.II, M.I.Red, M.I.Green)
-    U <- rbind(U.II, U.I.Red, U.I.Green)
-    rownames(M) <- rownames(U) <- c(snpProbesII, snpProbesI.Red$Name, snpProbesI.Green$Name)
-    beta <- M/(U+M+100)
-    return(beta)                               
-}
+              snpInfoII <- getProbeInfo(object, type="SnpII")
+              snpProbesII <- snpInfoII$Name
+              M.II <- getGreen(object)[snpInfoII$AddressA, , drop=FALSE]
+              U.II <- getRed(object)[snpInfoII$AddressA, , drop=FALSE]
+
+              snpInfoI <- getProbeInfo(object, type="SnpI")
+              snpProbesI.Green <- snpInfoI[snpInfoI$Color=="Grn", , drop=FALSE]
+              M.I.Green <- getGreen(object)[snpProbesI.Green$AddressB, , drop=F]
+              U.I.Green <- getGreen(object)[snpProbesI.Green$AddressA, , drop=F]
+              snpProbesI.Red <- snpInfoI[snpInfoI$Color=="Red", , drop=FALSE]
+              M.I.Red <- getRed(object)[snpProbesI.Red$AddressB, , drop=FALSE]
+              U.I.Red <- getRed(object)[snpProbesI.Red$AddressA, , drop=FALSE]
+
+              M <- rbind(M.II, M.I.Red, M.I.Green)
+              U <- rbind(U.II, U.I.Red, U.I.Green)
+              rsID <- c(snpProbesII, snpProbesI.Red$Name, snpProbesI.Green$Name)
+              rownames(M) <- rownames(U) <- rsID
+              beta <- M/(U+M+100) # I hate this.
+              return(beta)                               
+
+          })
 
 setMethod("getManifest", signature(object = "RGChannelSet"),
           function(object) {
@@ -148,12 +153,6 @@ setMethod("getBeta", signature(object = "RGChannelSet"),
               callGeneric(object, ...)
           })
 
-# wrap getSnpBeta function, for RGChannelSet objects 
-setMethod("getSNPs", signature(object = "RGChannelSet"),
-          function (object) {
-              getSnpBeta(object)
-          })
-
 setMethod("mapToGenome", signature(object = "RGChannelSet"),
           function(object, ...) {
               object <- preprocessRaw(object)
diff --git a/R/noobPipeline.R b/R/tcgaPipeline.R
similarity index 55%
rename from R/noobPipeline.R
rename to R/tcgaPipeline.R
index bf5e357..788926e 100644
--- a/R/noobPipeline.R
+++ b/R/tcgaPipeline.R
@@ -1,12 +1,10 @@
 # a "best practices" baseline for most studies
-noobPipeline <- function(rgSet, pCutoff=0.05) {
+tcgaPipeline <- function(rgSet, pCutoff=0.05) {
   pval <- detectionP(rgSet)
-  message("Running TCGA-style noob pipeline on ", ncol(rgSet), " samples...")
-  grSet <- mapToGenome(ratioConvert(preprocessNoob(rgSet)))
+  message("Running TCGA-style (noob) pipeline on ", ncol(rgSet), " samples...")
+  grSet <- ratioConvert(mapToGenome(preprocessNoob(rgSet)))
   message("Masking probes with detection p-value > ", pCutoff, "...")
   is.na(assays(grSet)$Beta) <- (pval[rownames(grSet),] >= pCutoff)
-  message("Dropping redundant \"M\" assay matrix...")
-  assays(grSet) <- assays(grSet)[c("Beta","CN")]
   message("Placing SNP probe betas in metadata(grSet)$SNPs...")
   metadata(grSet)$SNPs <- getSnpBeta(rgSet)
   message("Done.")
diff --git a/inst/unitTests/test_noobPipeline.R b/inst/unitTests/test_noobPipeline.R
deleted file mode 100644
index 5f18441..0000000
--- a/inst/unitTests/test_noobPipeline.R
+++ /dev/null
@@ -1,7 +0,0 @@
-test_noobPipeline <- function() {
-    stopifnot(require(minfiData))
-    grSetEx <- noobPipeline(updateObject(RGsetEx))
-    checkIdentical(getSNPs(grSetEx), getSNPs(updateObject(RGsetEx)))
-    checkIdentical(preprocessMethod(grSetEx), 
-                   c(mu.norm="Noob, dyeCorr=TRUE, dyeMethod=single")) 
-}
diff --git a/inst/unitTests/test_tcgaPipeline.R b/inst/unitTests/test_tcgaPipeline.R
new file mode 100644
index 0000000..d789d11
--- /dev/null
+++ b/inst/unitTests/test_tcgaPipeline.R
@@ -0,0 +1,7 @@
+test_tcgaPipeline <- function() {
+    stopifnot(require(minfiData))
+    grSetEx <- tcgaPipeline(updateObject(RGsetEx))
+    checkIdentical(getSnpBeta(grSetEx), getSnpBeta(updateObject(RGsetEx)))
+    checkIdentical(preprocessMethod(grSetEx), 
+                   c(mu.norm="Noob, dyeCorr=TRUE, dyeMethod=single")) 
+}
diff --git a/man/noobPipeline.Rd b/man/noobPipeline.Rd
deleted file mode 100644
index 4553a55..0000000
--- a/man/noobPipeline.Rd
+++ /dev/null
@@ -1,45 +0,0 @@
-\name{noobPipeline}
-\alias{noobPipeline}
-\alias{noobPipeline}
-\title{
-  A TCGA-style preprocessing pipeline for Infinium methylation microarrays.
-}
-\description{
-  The standard processing pipeline for the Cancer Genome Atlas (TCGA) was 
-  the methylumi implementation of preprocessNoob (which returns identical beta/M
-  values to the ssNoob implementation now standard in minfi).  Probes with 
-  detection p-values > 0.05 were masked as NA, SNP probes for label swap QC
-  tabulated, and the results uploaded as Level 2 data after certain masking 
-  steps (related to common SNPs and repetitive regions) had been applied.
-  This function wraps the individual steps to turn an \code{RGChannelSet} into 
-  a \code{GenomicRatioSet} directly comparable to canonical TCGA datasets. 
-}
-\usage{
-noobPipeline(rgSet, pCutoff=0.05)
-}
-\arguments{
-  \item{rgSet}{An object of class \code{RGChannelSet}.}
-  \item{pCutoff}{Above what detection pvalue should probes be marked NA? (0.05)}
-}
-\value{
-  An object of class \code{GenomicRatioSet} with additional SNP metadata.
-}
-\references{
-  TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund
-  \emph{Low-level processing of Illumina Infinium DNA Methylation
-    BeadArrays}.
-  Nucleic Acids Res (2013) 41, e90.
-  doi:\href{http://www.dx.doi.org/10.1093/nar/gkt090}{10.1093/nar/gkt090}.
-}
-\author{
-  Tim Triche, Jr.
-}
-\seealso{
-  \code{\linkS4class{RGChannelSet}}
-}
-\examples{
-if (require(minfiData)) {
-  grSetEx <- noobPipeline(RGsetEx)
-  identical(getSNPs(grSetEx), getSNPs(RGsetEx))
-}
-}
diff --git a/man/tcgaPipeline.Rd b/man/tcgaPipeline.Rd
new file mode 100644
index 0000000..64a6bcb
--- /dev/null
+++ b/man/tcgaPipeline.Rd
@@ -0,0 +1,53 @@
+\name{tcgaPipeline}
+\alias{tcgaPipeline}
+\alias{tcgaPipeline}
+\title{
+  A TCGA-style preprocessing pipeline for Infinium methylation microarrays.
+}
+\description{
+  The standard DNAme processing pipeline for the Cancer Genome Atlas (TCGA) was 
+  the methylumi implementation of preprocessNoob (which yields identical beta/M
+  values to the single-sample ssNoob implementation now standard in minfi, in 
+  the common case where a balanced reference sample was identified in each TCGA
+  batch). Probes with detection p-values > 0.05 were masked as NA, and SNP (rs)
+  probes included on each array by Illumina for label swap detection tabulated.
+  After QC and certain masking steps (related to common SNPs and repetitive 
+  regions) had been applied, the results were uploaded as Level 2 data for TCGA.
+  This function wraps the individual steps to turn an \code{RGChannelSet} into 
+  a \code{GenomicRatioSet} directly comparable to canonical TCGA datasets, save 
+  for the SNP/repeat masking steps (which, in hindsight, seem overzealous). The 
+  resulting GenomicRatioSet is thus directly comparable to processed TCGA data,
+  and as of this writing (May 2017), no single preprocessing method (let alone 
+  any single-sample preprocessing method) has emerged as superior for the
+  general case of mixed tumor and normal samples from varying tissues. Thus, 
+  this approach may also serve as a useful benchmark for methods development.
+}
+\usage{
+tcgaPipeline(rgSet, pCutoff=0.05)
+}
+\arguments{
+  \item{rgSet}{An object of class \code{RGChannelSet}.}
+  \item{pCutoff}{Above what detection pvalue should probes be marked NA? (0.05)}
+}
+\value{
+  An object of class \code{GenomicRatioSet} with additional SNP metadata.
+}
+\references{
+  TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund
+  \emph{Low-level processing of Illumina Infinium DNA Methylation
+    BeadArrays}.
+  Nucleic Acids Res (2013) 41, e90.
+  doi:\href{http://www.dx.doi.org/10.1093/nar/gkt090}{10.1093/nar/gkt090}.
+}
+\author{
+  Tim Triche, Jr.
+}
+\seealso{
+  \code{\linkS4class{RGChannelSet}}
+}
+\examples{
+if (require(minfiData)) {
+  grSetEx <- tcgaPipeline(RGsetEx)
+  stopifnot(identical(getSnpBeta(grSetEx), getSnpBeta(RGsetEx)))
+}
+}

From 2ddbdab2053c53c2b25421e07310e214ce156a0c Mon Sep 17 00:00:00 2001
From: ttriche <tim.triche@gmail.com>
Date: Wed, 10 May 2017 15:25:03 -0700
Subject: [PATCH 12/12] update manpage for preprocessNoob to reference
 tcgaPipeline

---
 man/preprocessNoob.Rd | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/man/preprocessNoob.Rd b/man/preprocessNoob.Rd
index b9f3a82..efdab02 100644
--- a/man/preprocessNoob.Rd
+++ b/man/preprocessNoob.Rd
@@ -10,8 +10,6 @@
 \usage{
 preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = TRUE,
                dyeMethod=c("single", "reference"))
-
-noobPipeline(rgSet, pCutoff = 0.01)
 }
 \arguments{
   \item{rgSet}{An object of class \code{RGChannelSet}.}
@@ -19,11 +17,9 @@ noobPipeline(rgSet, pCutoff = 0.01)
   \item{dyeCorr}{Should dye correction be done?}
   \item{verbose}{Should the function be verbose?}
   \item{dyeMethod}{How should dye bias correction be done: use a single sample approach (ssNoob), or a reference array?}
-  \item{pCutoff}{(for noobPipeline) Above what detection pvalue should probes be marked NA? (0.01)}
 }
 \value{
   For preprocessNoob, an object of class \code{MethylSet}.
-  For noobPipeline, an object of class \code{GenomicRatioSet} with SNP metadata.
 }
 \references{
   TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund
@@ -40,14 +36,14 @@ noobPipeline(rgSet, pCutoff = 0.01)
   as well as \code{\linkS4class{IlluminaMethylationManifest}} for the
   basic classes involved in these functions.
   \code{\link{preprocessRaw}} and \code{\link{preprocessQuantile}} are other preprocessing functions.
-  \code{\link{noobPipeline}} for an end-to-end processing pipeline with results directly comparable to the Cancer Genome Atlas (TCGA) DNA methylation data. 
+  \code{\link{tcgaPipeline}} for an end-to-end processing pipeline with results directly comparable to the Cancer Genome Atlas (TCGA) DNA methylation data. 
 }
 \examples{
 if (require(minfiData)) {
   ## RGsetEx.sub is a small subset of RGsetEx; 
   ## only used for computational speed.
   MsetEx.sub.noob <- preprocessNoob(RGsetEx.sub)
-  grSet.sub.noob <- noobPipeline(RGsetEx.sub)
+  grSet.sub.noob <- tcgaPipeline(RGsetEx.sub)
 }
 \dontrun{
 if (require(minfiData)) {