1. crlmm
  2. Commit a13f66d18720038fd2959ea4a43b26f4982a519e
Browse code

several updates for ff. new classes for affy/illumina processing. More s4-style code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45083 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/03/2010 04:46:55
Showing 29 changed files
CHANGES
History View file @ a13f66d
... ... 
@@ -413,3 +413,19 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
413 413
414 414 
 2010-03-05 M. Ritchie - committed version 1.5.29
415 415 
  * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd
416 
+
417 
+2010-03-07 R. Scharpf committed version 1.5.30
418 
+
419 
+- one can use ff in conjunction with affy platforms 5.0 and 6.0
420 
+
421 
+- more s4-style code
422 
+
423 
+- preprocessing / genotyping is basically the same set of commands with either illumina/affy platforms (though illumina-users may have to play with some of the options for reading idat files
424 
+
425 
+- if ff package is loaded, the assayData elements are ff objects
426 
+
427 
+- the classes all inherit from 'CrlmmContainer' that contains an additional slot 'options' and 'genomeAnnotation'.   options is a list with the default arguments to snprma, crlmm, etc, as well as a few global settings such as 'verbose' and 'seed'.  I added the genomeAnnotation slot simply because I want to be able to use ff-objects for the feature-level data.   Maybe with setClassUnion we could avoid adding the genomeAnnotation slot (and use featureData instead), but I didn't have much success with this.
428 
+
429 
+- the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.
430 
+
431 
+- The crlmm.Rd file contains an example with / without ff for Affymetrix data.
DESCRIPTION
History View file @ a13f66d
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.5.29
5 
-Date: 2010-03-05
4 
+Version: 1.5.30
5 
+Date: 2010-03-07
6 6 
 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
7 7 
 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -19,16 +19,21 @@ Imports: affyio (>= 1.15.2),
19 19 
          splines,
20 20 
          mvtnorm,
21 21 
          ellipse,
22 
-         SNPchip
23 
-Enhances: ff
22 
+         SNPchip,ff
24 23 
 Suggests: hapmapsnp5,
25 24 
           hapmapsnp6,
26 25 
           genomewidesnp5Crlmm (>= 1.0.2),
27 26 
           genomewidesnp6Crlmm (>= 1.0.2),
28 27 
           snpMatrix,
29 28 
           metaArray
30 
-Collate: AllGenerics.R
29 
+Collate: AllClasses.R
30 
+	 AllGenerics.R
31 
+	 methods-AffymetrixAlleleSet.R
32 
+	 methods-IlluminaAlleleSet.R
33 
+	 methods-CrlmmContainer.R
31 34 
 	 methods-CNSet.R
35 
+	 methods-AlleleSet.R
36 
+	 methods-CallSet.R
32 37 
 	 methods-eSet.R
33 38 
          methods-SnpSuperSet.R
34 39 
          cnrma-functions.R
NAMESPACE
History View file @ a13f66d
... ... 
@@ -8,11 +8,12 @@ importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
8 8
9 9 
 importMethodsFrom(Biobase, annotation, "annotation<-",
10 10 
                   annotatedDataFrameFrom, assayData, "assayData<-",
11 
+		  snpCallProbability,
11 12 
                   combine, dims, experimentData, "experimentData<-",
12 13 
                   fData, featureData, "featureData<-", featureNames,
13 14 
                   fvarMetadata, fvarLabels, pData, phenoData,
14 15 
                   "phenoData<-", protocolData, "protocolData<-",
15 
-                  pubMedIds, rowMedians, sampleNames, storageMode,
16 
+                  pubMedIds, rowMedians, sampleNames, snpCall, storageMode,
16 17 
                   "storageMode<-", updateObject, varLabels)
17 18
18 19 
 importFrom(Biobase, assayDataElement, assayDataElementNames,
... ... 
@@ -20,11 +21,16 @@ importFrom(Biobase, assayDataElement, assayDataElementNames,
20 21 
            validMsg)
21 22
22 23 
 ## oligoClasses
23 
-importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)
24 
+##importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
24 25
25 
-importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
26 
-		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
27 
-		  chromosome, position, CA, "CA<-", CB, "CB<-", A, B)
26 
+##S3 method ffdf and class ffdf
27 
+importFrom(ff, ffdf, ff, as.ff, as.ffdf)
28 
+
29 
+
30 
+
31 
+##importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
32 
+##		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
33 
+##		  chromosome, position, CA, "CA<-", CB, "CB<-", A, B)
28 34
29 35 
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
30 36 
            copyNumber)
... ... 
@@ -60,8 +66,24 @@ importFrom(mvtnorm, dmvnorm)
60 66 
 ## ellipse
61 67 
 importFrom(ellipse, ellipse)
62 68
63 
-exportMethods(copyNumber)
64 
-export(cnOptions, crlmm, crlmmIllumina, crlmmIlluminaV2, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam)
69 
+
70 
+##exportClasses(FFSet)
71 
+exportMethods(annotatedDataFrameFrom,
72 
+	copyNumber, initialize,
73 
+              ##show, "$", "[[", "[",
74 
+	      genomeAnnotation,
75 
+	      lM,
76 
+	      CA,
77 
+	      CB,
78 
+	      A,
79 
+	      B,
80 
+	      snpCall,
81 
+	      confs,
82 
+	      chromosome,
83 
+	      position,
84 
+	      isSnp)
85 
+export(crlmmOptions, crlmm, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam, validCdfNames)
86 
+
65 87
66 88
67 89 
 #############
... ... 
@@ -69,10 +91,5 @@ export(cnOptions, crlmm, crlmmIllumina, crlmmIlluminaV2, crlmmCopynumber, ellips
69 91 
 #############
70 92
71 93 
 ##export everything that does not start with a .
72 
-##exportPattern("^[^\\.]")
94 
+exportPattern("^[^\\.]")
73 95
74 
-##export(thresholdModelParams, computeCopynumber.CNSet, nuphiAllele, coefs, biasAdjNP,
75 
-##       nonpolymorphic.poe, crlmmWrapper,
76 
-##       loadIlluminaCallSet, loadIlluminaRG, loadIlluminaCnrma,
77 
-##       cnrma,
78 
-##       crlmmGT, oneBatch)
R/AllClasses.R
History View file @ a13f66d
79 96 
new file mode 100644
... ... 
@@ -0,0 +1,74 @@
1 
+setOldClass("ffdf")
2 
+setOldClass("ff_matrix")
3 
+setClassUnion("matrix_or_ff", c("matrix", "ff_matrix"))
4 
+setClassUnion("list_or_ffdf", c("list", "ffdf"))
5 
+setClass("CrlmmContainer", contains="eSet",
6 
+	 representation(options="list",
7 
+			genomeAnnotation="ANY",
8 
+			"VIRTUAL"))
9 
+
10 
+setMethod("show", "CrlmmContainer", function(object){
11 
+	callNextMethod(object)
12 
+	cat("options: \n")
13 
+	print(names(crlmmOptions(object)))
14 
+	cat("\n")
15 
+	cat("genomeAnnotation:", nrow(genomeAnnotation(object)), " rows, ", ncol(genomeAnnotation(object)), " columns\n")
16 
+	print(genomeAnnotation(object)[1:5, ])
17 
+	cat("\n")
18 
+})
19 
+setClass("AlleleSet", contains="CrlmmContainer")
20 
+setClass("CallSet", contains="AlleleSet")
21 
+setClass("CNSet", contains="CallSet",
22 
+	 representation(lM="list_or_ffdf"))
23 
+
24 
+setClass("IlluminaRGSet", contains="CrlmmContainer")
25 
+setClass("IlluminaXYSet", contains="CrlmmContainer")
26 
+
27 
+setClass("AffymetrixAlleleSet", contains="AlleleSet")  ##AffymetrixAlleleSet
28 
+setClass("IlluminaAlleleSet", contains="AlleleSet")
29 
+##setClass("AffymetrixBigData", contains="AffymetrixAlleleSet")
30 
+##setClass("AffymetrixSmallData", contains="AffymetrixAlleleSet")
31 
+##setClass("IlluminaSmallData", contains="IlluminaAlleleSet")
32 
+##setClass("IlluminaBigData", contains="IlluminaAlleleSet")
33 
+##setMethod("initialize", "AffymetrixBigData", function(.Object, annotation){
34 
+##	.Object <- callNextMethod(.Object)
35 
+##	if(!missing(annotation)) annotation(.Object) <- annotation
36 
+##	.Object
37 
+##})
38 
+##setClass("AffymetrixCallSet", contains="CallSet")
39 
+##setClass("IlluminaCallSet", contains="CallSet")
40 
+setMethod("initialize", "AlleleSet", function(.Object, alleleA=new("matrix"), alleleB=new("matrix"), ...){
41 
+	.Object <- callNextMethod(.Object, alleleA=alleleA, alleleB=alleleB, ...)
42 
+	storageMode(.Object) <- "environment"
43 
+	.Object
44 
+})
45 
+setMethod("initialize", "CallSet", function(.Object, call=new("matrix"), callProbability=new("matrix"), ...){
46 
+	.Object <- callNextMethod(.Object, call=call, callProbability=callProbability, ...)
47 
+	storageMode(.Object) <- "environment"
48 
+	.Object
49 
+})
50 
+setMethod("initialize", "CNSet", function(.Object, CA=new("matrix"), CB=new("matrix"), lM=new("list"), ...){
51 
+	.Object <- callNextMethod(.Object, CA=CA, CB=CB, lM=lM,...)
52 
+	storageMode(.Object) <- "environment"
53 
+	.Object
54 
+})
55 
+setValidity("AlleleSet", function(object) {
56 
+	assayDataValidMembers(assayData(object), c("alleleA", "alleleB"))
57 
+})
58 
+setValidity("IlluminaRGSet", function(object) {
59 
+	assayDataValidMembers(assayData(object), c("R", "G", "zero"))
60 
+})
61 
+setValidity("IlluminaXYSet", function(object) {
62 
+	assayDataValidMembers(assayData(object), c("X", "Y", "zero"))
63 
+})
64 
+
65 
+setValidity("CallSet", function(object) {
66 
+	assayDataValidMembers(assayData(object), c("alleleA", "alleleB", "call", "callProbability"))
67 
+})
68 
+setValidity("CNSet", function(object) {
69 
+	assayDataValidMembers(assayData(object), c("alleleA", "alleleB", "call", "callProbability", "CA", "CB"))
70 
+})
71 
+
72 
+
73 
+
74 
+
R/AllGenerics.R
History View file @ a13f66d
... ... 
@@ -1,12 +1,57 @@
1 
-##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
-##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
1 
+setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
+setGeneric("B<-", function(object, value) standardGeneric("B<-"))
3 3
4 4 
 setGeneric("getParam", function(object, name, ...) standardGeneric("getParam"))
5 5 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
6 6 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
7 
-setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
7 
+setGeneric("confs", function(object) standardGeneric("confs"))
8 
+setGeneric("computeCopynumber", function(object) standardGeneric("computeCopynumber"))
9 
+setGeneric("crlmm", function(object, ...) standardGeneric("crlmm"))
10 
+setGeneric("crlmmOptions", function(object) standardGeneric("crlmmOptions"))
11 
+setGeneric("crlmmOptions<-", function(object, value) standardGeneric("crlmmOptions<-"))
12 
+setGeneric("construct", function(object, filenames) standardGeneric("construct"))
13 
+
14 
+setGeneric("getOptions", function(object) standardGeneric("getOptions"))
15 
+
16 
+##setGeneric("getA", function(object) standardGeneric("getA"))
17 
+##setGeneric("getB", function(object) standardGeneric("getB"))
18 
+##setGeneric("getG", function(object) standardGeneric("getG"))
19 
+##setGeneric("getR", function(object) standardGeneric("getR"))
20 
+##setGeneric("getZero", function(object) standardGeneric("getZero"))
21 
+##setGeneric("getCalls", function(object) standardGeneric("getCalls"))
22 
+##setGeneric("getConfs", function(object) standardGeneric("getConfs"))
23 
+##setGeneric("getCA", function(object) standardGeneric("getCA"))
24 
+##setGeneric("getCB", function(object) standardGeneric("getCB"))
25 
+setGeneric("getPhenoData", function(object) standardGeneric("getPhenoData"))
26 
+setGeneric("getFeatureData", function(object) standardGeneric("getFeatureData"))
27 
+setGeneric("getProtocolData", function(object, filenames) standardGeneric("getProtocolData"))
28 
+setGeneric("getGenomeAnnotation", function(object, ...) standardGeneric("getGenomeAnnotation"))
29 
+setGeneric("getLinearModelParam", function(object, ...) standardGeneric("getLinearModelParam"))
30 
+
31 
+##setGeneric("initializeStorage", function(object) standardGeneric("initializeStorage"))
32 
+setGeneric("prediction", function(x, ...) standardGeneric("prediction"))
33 
+setGeneric("genomeAnnotation", function(object) standardGeneric("genomeAnnotation"))
34 
+setGeneric("genomeAnnotation<-", function(object,value) standardGeneric("genomeAnnotation<-"))
35 
+setGeneric("lM", function(object) standardGeneric("lM"))
36 
+setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
37 
+
38 
+##setGeneric("nFeatures", function(object) standardGeneric("nFeatures"))
39 
+
8 40 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
41 
+setGeneric("rma", function(object) standardGeneric("rma"))
42 
+setGeneric("snprma", function(object, ...) standardGeneric("snprma"))
9 43 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
10 44 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
11 45 
 ##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
12 46
47 
+setGeneric("R", function(object) standardGeneric("R"))
48 
+setGeneric("G", function(object) standardGeneric("G"))
49 
+setGeneric("Z", function(object) standardGeneric("Z"))
50 
+setGeneric("X", function(object) standardGeneric("X"))
51 
+setGeneric("Y", function(object) standardGeneric("Y"))
52 
+setMethod("R", "IlluminaRGSet", function(object) assayDataElement(object, "R"))
53 
+setMethod("G", "IlluminaRGSet", function(object) assayDataElement(object, "G"))
54 
+setMethod("Z", "IlluminaRGSet", function(object) assayDataElement(object, "zero"))
55 
+setMethod("X", "IlluminaXYSet", function(object) assayDataElement(object, "X"))
56 
+setMethod("Y", "IlluminaXYSet", function(object) assayDataElement(object, "Y"))
57 
+setMethod("Z", "IlluminaXYSet", function(object) assayDataElement(object, "zero"))
R/cnrma-functions.R
History View file @ a13f66d
... ... 
@@ -153,366 +153,272 @@ predictGender <- function(res, cdfName="genomewidesnp6", SNRMin=5){
153 153 
 	return(gender)
154 154 
 }
155 155
156 
-##crlmmCopynumber <- function(filenames, cnOptions, object, ...){
157 
-##	if(!missing(object)){
158 
-##		stopifnot(class(object) == "CNSet")
159 
-##		createIntermediateObjects <- FALSE
160 
-##	} else {
161 
-##		createIntermediateObjects <- TRUE
162 
-##		## 33G for 1239 files
163 
-##		crlmmResults <- crlmmWrapper(filenames, cnOptions, ...)
164 
-##		snprmaResult <- crlmmResults[["snprmaResult"]]
165 
-##		cnrmaResult <- crlmmResults[["cnrmaResult"]]
166 
-##		callSet <- crlmmResults[["callSet"]]
167 
-##		rm(crlmmResults); gc()
168 
-##		annotation(callSet) <- cnOptions[["cdfName"]]
169 
-##		stopifnot(identical(featureNames(callSet), snprmaResult[["gns"]]))
170 
-##		path <- system.file("extdata", package=paste(annotation(callSet), "Crlmm", sep=""))
156 
+
157 
+##initializeFFObjects <- function(filenames, cnOptions){
158 
+##	outdir <- cnOptions[["outdir"]]
159 
+##	cdfName <- cnOptions[["cdfName"]]
160 
+##	AFile <- cnOptions[["AFile"]]
161 
+##	BFile <- cnOptions[["BFile"]]
162 
+##	callsFile <- cnOptions[["callsFile"]]
163 
+##	confsFile <- cnOptions[["confsFile"]]
164 
+##	snprmaFile <- cnOptions[["snprmaFile"]]
165 
+##	cnrmaFile <- cnOptions[["cnrmaFile"]]
166 
+##	CAFile <- cnOptions[["CAFile"]]
167 
+##	CBFile <- cnOptions[["CBFile"]]
168 
+##	load.it <- cnOptions[["load.it"]]
169 
+##	fileExists <- list(A=file.exists(AFile),
170 
+##			   B=file.exists(BFile),
171 
+##			   calls=file.exists(callsFile),
172 
+##			   confs=file.exists(confsFile),
173 
+##			   CA=file.exists(CAFile),
174 
+##			   CB=file.exists(CBFile))
175 
+##	allExists <- all(unlist(fileExists))
176 
+##	##if files already exist, check that the files have the appropriate dimension
177 
+##	if(allExists){
178 
+##		load(AFile)
179 
+##		open(A)
180 
+##		sns <- dimnames(A)[[2]]
181 
+##		if(!identical(sns, basename(filenames)) | !load.it){
182 
+##		## if not of the same dimension, clean up
183 
+##			message("Sample names in previously saved objects differ from the filenames. Removing previously saved objects.")
184 
+##			delete(A); gc()
185 
+##			unlink(AFile)
186 
+##			load(BFile); delete(B); unlink(BFile)
187 
+##			unlink(snprmaFile)
188 
+##			unlink(cnrmaFile)
189 
+##			if(file.exists(file.path(outdir, "cnParams.rda"))){
190 
+##				load(file.path(outdir, "cnParams.rda"))
191 
+##				delete(cnParams); gc()
192 
+##				unlink(file.path(outdir, "cnParams.rda"))
193 
+##			}
194 
+##			load(callsFile); delete(calls); unlink(callsFile)
195 
+##			load(confsFile); delete(confs); unlink(confsFile)
196 
+##			load(CAFile); delete(CA); unlink(CAFile)
197 
+##			load(CBFile); delete(CB); unlink(CBFile)
198 
+##			allExists <- FALSE
199 
+##		}
200 
+##	}
201 
+##	if(!allExists) 	{
202 
+##		message("Initializing ff objects for A, B, confs, calls, CA, and CB.")
203 
+##		dns <- .dimnames(filenames, cnOptions[["cdfName"]], cnOptions[["verbose"]])
204 
+##		fns <- dns[[1]]
205 
+##	}
206 
+##	if(!file.exists(AFile)) {A <- initializeBigMatrix(dns); save(A, file=AFile); close(A)}
207 
+##	if(!file.exists(BFile)) {B <- initializeBigMatrix(dns); save(B, file=BFile); close(B)}
208 
+##	if(!file.exists(confsFile)) {confs <- initializeBigMatrix(dns); save(confs, file=confsFile); close(confs)}
209 
+##	if(!file.exists(callsFile)) {calls <- initializeBigMatrix(dns); save(calls, file=callsFile); close(calls)}
210 
+##	if(!file.exists(CAFile)) {CA <- initializeBigMatrix(dns); save(CA, file=CAFile); close(CA)}
211 
+##	if(!file.exists(CBFile)) {CB <- initializeBigMatrix(dns); save(CB, file=CBFile); close(CB)}
212 
+##	featureDataFile <- file.path(outdir, "featureDataFF.rda")
213 
+##	if(!file.exists(featureDataFile)){
214 
+##		path <- system.file("extdata", package=paste(cnOptions[["cdfName"]], "Crlmm", sep=""))
171 215 
 ##		load(file.path(path, "snpProbes.rda"))
172 216 
 ##		snpProbes <- get("snpProbes")
173 217 
 ##		load(file.path(path, "cnProbes.rda"))
174 
-##		cnProbes <- get("cnProbes")
175 
-##		k <- grep("chr", colnames(snpProbes))
176 
-##		if(length(k) < 1) stop("chr or chromosome not in colnames(snpProbes)")
218 
+##		cnProbes <- get("cnProbes")
219 
+##		message("Initializing featureDataFF.")
220 
+##		fvarlabels <- c("chromosome", "position",   "isSnp")
221 
+##		M <- matrix(NA, length(fns), 3, dimnames=list(fns, fvarlabels))
222 
+##		index <- match(rownames(snpProbes), rownames(M)) #only snp probes in M get assigned position
223 
+##		M[index, "position"] <- snpProbes[, grep("pos", colnames(snpProbes))]
224 
+##		M[index, "chromosome"] <- snpProbes[, grep("chr", colnames(snpProbes))]
225 
+##		M[index, "isSnp"] <- 1L
226 
+##		index <- match(rownames(cnProbes), rownames(M)) #only snp probes in M get assigned position
227 
+##		M[index, "position"] <- cnProbes[, grep("pos", colnames(cnProbes))]
228 
+##		M[index, "chromosome"] <- cnProbes[, grep("chr", colnames(cnProbes))]
229 
+##		M[index, "isSnp"] <- 0L
230 
+##		featureDataFF <- ff(M, dim=c(nrow(M), ncol(M)),
231 
+##				    vmode="integer", finalizer="close",
232 
+##				    overwrite=TRUE,
233 
+##				    dimnames=list(fns, fvarlabels))
234 
+##		save(featureDataFF, file=file.path(outdir, "featureDataFF.rda"))
235 
+##		close(featureDataFF)
236 
+##		rm(M, cnProbes, snpProbes, featureDataFF); gc()
177 237 
 ##	}
238 
+##	## parameters file
239 
+##	parameterFile <- file.path(outdir, "cnParams.rda")
240 
+##	if(!file.exists(parameterFile)) {
241 
+##		message("Initializing parameters file")
242 
+##		batch <- cnOptions[["batch"]]
243 
+##		dns.batch <- list(fns, unique(batch))
244 
+##		cnParams <- initializeParamObject(dns.batch)
245 
+##		save(cnParams, file=file.path(outdir, "cnParams.rda"))
246 
+##		close(cnParams)
247 
+##	}
248 
+##}
249 
+
250 
+##preprocessAndGenotype <- function(filenames, cnOptions, ...){
178 251 
 ##	set.seed(cnOptions[["seed"]])  ##for reproducibility
179 
-##	cnFile <- cnOptions[["cnFile"]]
180 
-##	chromosome <- cnOptions[["chromosome"]]
181 
-##	SNRmin <- cnOptions[["SNRmin"]]
252 
+##	protocolFile <- cnOptions[["protocolFile"]]
253 
+##	cdfName <- cnOptions[["cdfName"]]
254 
+##	verbose <- cnOptions[["verbose"]]
255 
+##	if(file.exists(protocolFile)){
256 
+##		## check that file is the same dimension
257 
+##		load(protocolFile)
258 
+##		if(!identical(sampleNames(protocoldata), basename(filenames)))
259 
+##			unlink(protocolFile)
260 
+##	}
261 
+##	if(!file.exists(protocolFile)){
262 
+##		platform <- whichPlatform(paste(cdfName, "Crlmm", sep=""))
263 
+##		if(platform=="affymetrix"){
264 
+##			if(verbose) message("Creating protocol file with scan dates for the affy arrays")
265 
+##			scanDates <- data.frame(ScanDate=sapply(filenames, celfileDate))
266 
+##			rownames(scanDates) <- basename(rownames(scanDates))
267 
+##			protocoldata <- new("AnnotatedDataFrame",
268 
+##					    data=scanDates,
269 
+##					    varMetadata=data.frame(labelDescription=colnames(scanDates),
270 
+##					    row.names=colnames(scanDates)))
271 
+##			save(protocoldata, file=protocolFile)
272 
+##		}
273 
+##		## protocol file for illumina saved during the readIdatFile step
274 
+##	}
275 
+##	if(isPackageLoaded("ff")) initializeFFObjects(filenames, cnOptions)
276 
+##	crlmmWrapper(filenames, cnOptions, ...)
277 
+##	message("Checking for required files...")
278 
+##	message(cnOptions[["AFile"]], ": ", file.exists(cnOptions[["AFile"]]))
279 
+##	message(cnOptions[["BFile"]], ": ", file.exists(cnOptions[["BFile"]]))
280 
+##	message(cnOptions[["callsFile"]], ": ", file.exists(cnOptions[["callsFile"]]))
281 
+##	message(cnOptions[["confsFile"]], ": ", file.exists(cnOptions[["confsFile"]]))
282 
+##	message(cnOptions[["snprmaFile"]], ": ", file.exists(cnOptions[["snprmaFile"]]))
283 
+##	message(cnOptions[["protocolFile"]], ": ", file.exists(cnOptions[["protocolFile"]]))
284 
+##}
285 
+
286 
+##crlmmCopynumber <- function(cnOptions, ...){
287 
+##crlmmCopynumber <- function(object){
288 
+##	ops <- crlmmOptions(object)
289 
+##	verbose <- ops$verbose
290 
+##	calls <- snpCall(object)
291 
+##	confs <- confs(object)
292 
+##	fns <- featureNames(object)
293 
+##	SNRmin <- ops$SNRMin
294 
+##	batch <- object$batch
295 
+##	whichBatch <- ops$cnOpts$whichBatch
296 
+##	chromosome <- ops$cnOpts$chromosome
297 
+##	MIN.SAMPLES <- ops$cnOpts$MIN.SAMPLES
298 
+##	##k <- grep("chr", colnames(snpProbes))
182 299 
 ##	for(CHR in chromosome){
300 
+##		##annotated snp and cn probes
301 
+##		##snps <- rownames(snpProbes)[snpProbes[, k] == CHR]
302 
+##		##cns <- rownames(cnProbes)[cnProbes[, k] == CHR]
303 
+##		##where are the annotated snps in the fns file
304 
+##		##index.snps <- match(snps, fns)
305 
+##		##index.cn <- match(cns, fns)
306 
+##		##row.index <- c(index.snps, index.cn)
183 307 
 ##		cat("Chromosome ", CHR, "\n")
184 
-##		if(createIntermediateObjects){
185 
-##			snps <- rownames(snpProbes)[snpProbes[, k] == CHR]
186 
-##			cnps <- rownames(cnProbes)[cnProbes[, k] == CHR]
187 
-##			index.snps <- match(snps, featureNames(callSet))
188 
-##			index.nps <- match(cnps, rownames(cnrmaResult[["NP"]]))
189 
-##			if(!is.null(cnrmaResult)){
190 
-##				npI <- cnrmaResult$NP[index.nps, ]
191 
-##			} else npI <- NULL
192 
-##			snpI <- list(A=snprmaResult$A[index.snps, ],
193 
-##				     B=snprmaResult$B[index.snps, ],
194 
-##				     sns=snprmaResult$sns,
195 
-##				     gns=snprmaResult$gns[index.snps],
196 
-##				     SNR=snprmaResult$SNR,
197 
-##				     SKW=snprmaResult$SKW,
198 
-##				     mixtureParams=snprmaResult$mixtureParams,
199 
-##				     cdfName=snprmaResult$cdfName)
200 
-##			cnOptions[["batch"]] <- cnOptions[["batch"]][snpI[["SNR"]]  >= SNRmin]
201 
-##			cnSet <- combineIntensities(res=snpI,
202 
-##						    NP=npI,
203 
-##						    callSet=callSet[index.snps, ])
204 
-##			if(any(cnSet$SNR > SNRmin)){
205 
-##				message(paste("Excluding samples with SNR < ", SNRmin))
206 
-##				cnSet <- cnSet[, cnSet$SNR >= SNRmin]
207 
-##			}
208 
-##			rm(snpI, npI, snps, cnps, index.snps, index.nps); gc()
209 
-##			pData(cnSet)$batch <- cnOptions[["batch"]]
210 
-##			featureData(cnSet) <- lm.parameters(cnSet, cnOptions)
211 
-##		} else {
212 
-##			cnSet <- object
213 
-##		}
214 
-##		if(CHR != 24){
215 
-##			## 60G for 1239 files
216 
-##			cnSet <- computeCopynumber(cnSet, cnOptions)
217 
-##		} else{
218 
-##			message("Copy number estimates not available for chromosome Y.  Saving only the 'callSet' object for this chromosome")
219 
-##			alleleSet <- cnSet
220 
-##			save(alleleSet, file=file.path(cnOptions[["outdir"]], paste("alleleSet_", CHR, ".rda", sep="")))
221 
-##			rm(cnSet, alleleSet); gc()
222 
-##			next()
223 
-##		}
224 
-##		if(length(chromosome) == 1){
225 
-##			if(cnOptions[["save.cnset"]]){
226 
-##				save(cnSet, file=file.path(paste(cnFile, "_", CHR, ".rda", sep="")))
227 
-##				##save(cnSet, file=file.path(cnOptions[["outdir"]], paste("cnSet_", CHR, ".rda", sep="")))
308 
+##		for(i in whichBatch){
309 
+##			PLATE <- unique(batch)[i]
310 
+##			message("Plate: ", PLATE)
311 
+##			sample.index <- which(batch==PLATE)
312 
+##			if(length(sample.index) < MIN.SAMPLES) {
313 
+##				warning("Plate ", PLATE, " has fewer than 10 samples.  Skipping this plate.")
314 
+##				next()
228 315 
 ##			}
229 
-##		}
230 
-##		if(length(chromosome) > 1){
231 
-##			message(paste("Saving ", file.path(cnOptions[["outdir"]], paste(cnFile, "_", CHR, ".rda", sep=""))))
232 
-##			save(cnSet, file=file.path(paste(cnFile, "_", CHR, ".rda", sep="")))
233 
-##			##save(cnSet, file=file.path(cnOptions[["outdir"]], paste("cnSet_", CHR, ".rda", sep="")))
234 
-##			rm(cnSet); gc()
235 
-##		} else {
236 
-##			return(cnSet)
237 
-##		}
238 
-##	}
239 
-##	saved.objects <- list.files(cnOptions[["outdir"]], pattern=cnFile, full.names=TRUE)
240 
-##	return(saved.objects)
316 
+##			##cnOptions[["batch"]] <- cnOptions[["batch"]][snpI[["SNR"]]  >= SNRmin]
317 
+####			if(isPackageLoaded("ff")){
318 
+####				ca <- as.matrix(CA[row.index, sample.index])
319 
+####				cb <- as.matrix(CB[row.index, sample.index])
320 
+####			} else{
321 
+####				dns <- dimnames(A[row.index, sample.index])
322 
+####				cb <- ca <- matrix(NA, nr=length(row.index), nc=length(sample.index), dimnames=dns)
323 
+####			}
324 
+####			cnSet <- new("CNSet",
325 
+####				     alleleA=as.matrix(A[row.index, sample.index]),
326 
+####				     alleleB=as.matrix(B[row.index, sample.index]),
327 
+####				     call=as.matrix(calls[row.index, sample.index]),
328 
+####				     callProbability=as.matrix(confs[row.index, sample.index]),
329 
+####				     CA=ca,
330 
+####				     CB=cb,
331 
+####				     featureData=annotatedDataFrameFrom(as.matrix(A[row.index, sample.index]), byrow=TRUE),
332 
+####				     phenoData=pD[sample.index, ],
333 
+####				     protocolData=protocoldata[sample.index, ])
334 
+##			##Verify this is correct
335 
+####			annotation(cnSet) <- cnOptions[["cdfName"]]
336 
+####			featureNames(cnSet) <- fns[row.index]
337 
+##			##add chromosome, position, isSnp
338 
+####			cnSet <- annotate(cnSet)
339 
+####			if(any(cnSet$SNR > SNRmin)){
340 
+####				if(CHR == chromosome[1]) message(paste("Excluding samples with SNR < ", SNRmin))
341 
+####				cnSet <- cnSet[, cnSet$SNR >= SNRmin]
342 
+####			}
343 
+####			featureData(cnSet) <- lm.parameters(cnSet, cnOptions)
344 
+##			if(CHR > 23) next()
345 
+##			cnSet <- computeCopynumber(object[chromosome(object) == CHR, sample.index])
346 
+####			if(!isPackageLoaded("ff") & i == whichBatch[1]) cnParams <- initializeParamObject(list(featureNames(cnSet), unique(cnOptions[["batch"]])[whichBatch]))
347 
+####			if(!isPackageLoaded("ff")) {
348 
+####				row.index <- 1:nrow(cnSet)
349 
+####			} else {
350 
+####				##Warning message:
351 
+####				##In d[[1]] * d[[2]] : NAs produced by integer overflow
352 
+####				CA[row.index, sample.index] <- cnSet@assayData[["CA"]]
353 
+####				CB[row.index, sample.index] <- cnSet@assayData[["CB"]]
354 
+####			}
355 
+####			cnParams <- updateParams(cnParams, cnSet, row.index, batch=unique(batch)[i])
356 
+##			## keep only chromosome, position, and isSnp
357 
+####			featureData(cnSet) <- featureData(cnSet)[, 1:3]
358 
+####			if(!isPackageLoaded("ff")){
359 
+####				save(cnSet, file=paste(cnFile, "_", PLATE, "_", CHR, ".rda", sep=""))
360 
+####				save(cnParams, file=paste(outdir, "cnParams_", PLATE, "_", CHR, ".rda", sep=""))
361 
+####			}
362 
+##		} ## end of batch loop
363 
+##	} ## end of chromosome loop
364 
+####	if(isPackageLoaded("ff")) {
365 
+####		close(cnParams)
366 
+####		close(A); close(B)
367 
+####		close(CA); close(CB)
368 
+####		save(CA, file=CAFile)
369 
+####		save(CB, file=CBFile)
370 
+####		close(calls); close(confs)
371 
+####		return()
372 
+####	}
373 
+##	return(cnSet)
241 374 
 ##}
242 375
243 376
244 377
245 
-##crlmmCopynumber <- function(filenames, cnOptions, object, ...){
246 
-##	cnOpts <- cnOptions
247 
-##	batchSize <- cnOptions[["crlmmBatchSize"]]
248 
-##	batch <- cnOptions[["batch"]]
249 
-##	outdir <- cnOptions[["outdir"]]
250 
-##	##if necessary, split plates in separate batches
251 
-##	if(length(filenames) > batchSize){
252 
-##		L <- length(table(batch))
253 
-##		message("Processing the files in")
254 
-##		batchList <- split(names(table(batch)), rep(1:L, each=10, length.out=L))
255 
-##		for(i in seq(along=batchList)){
256 
-##			index <- as.character(batch) %in% as.character(batchList[[i]])
257 
-##			fns <- filenames[index]
258 
-##			cnOpts[["batch"]] <- cnOptions[["batch"]][index]
259 
-##			cnOpts[["AFile"]] <- paste(outdir, "/", paste(cnOptions[["AFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
260 
-##			cnOpts[["BFile"]] <- paste(outdir, "/", paste(cnOptions[["BFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
261 
-##			cnOpts[["CAFile"]] <- paste(outdir, "/", paste(cnOptions[["CAFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
262 
-##g			cnOpts[["CBFile"]] <- paste(outdir, "/", paste(cnOptions[["CBFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
263 
-##			cnOpts[["callsFile"]] <- paste(outdir, "/", paste(cnOptions[["callsFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
264 
-##			cnOpts[["confsFile"]] <- paste(outdir, "/", paste(cnOptions[["confsFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
265 
-##			cnOpts[["snprmaFile"]] <- paste(outdir, "/", paste(cnOptions[["snprmaFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
266 
-##			cnOpts[["cnrmaFile"]] <- paste(outdir, "/", paste(cnOptions[["cnrmaFile"]], i, sep="_crlmmBatch"), ".rda", sep="")
267 
-##			cnOpts[["cnFile"]] <- file.path(outdir, paste(cnOptions[["cnFile"]], i, sep="_crlmmBatch"))
268 
-##			cnOpts[["rgFile"]] <- file.path(outdir, paste(cnOptions[["rgFile"]], i, sep="_crlmmBatch"))
269 
-##			crlmmCopynumber.crlmmBatch(fns, cnOpts, object, ...)
270 
-##		}
271 
-##	} else {
272 
-##		cnOpts[["AFile"]] <- paste(outdir, "/", cnOptions[["AFile"]], ".rda", sep="")
273 
-##		cnOpts[["BFile"]] <- paste(outdir, "/", cnOptions[["BFile"]], ".rda", sep="")
274 
-##		cnOpts[["callsFile"]] <- paste(outdir, "/", cnOptions[["callsFile"]], ".rda", sep="")
275 
-##		cnOpts[["confsFile"]] <- paste(outdir, "/", cnOptions[["confsFile"]], ".rda", sep="")
276 
-##		cnOpts[["snprmaFile"]] <- paste(outdir, "/",cnOptions[["snprmaFile"]], ".rda", sep="")
277 
-##		cnOpts[["cnrmaFile"]] <- paste(outdir, "/", cnOptions[["cnrmaFile"]], ".rda", sep="")
278 
-##		cnOpts[["cnFile"]] <- file.path(outdir, cnOptions[["cnFile"]])
279 
-##		cnOpts[["rgFile"]] <- file.path(outdir, cnOptions[["rgFile"]])
280 
-##		crlmmCopynumber.crlmmBatch(filenames, cnOpts, object, ...)
281 
-##	}
282 
-##}
283 378
284 379
285 
-crlmmCopynumber <- function(filenames, cnOptions, object, ...){
286 
-	set.seed(cnOptions[["seed"]])  ##for reproducibility
287 
-	if(!missing(object)){
288 
-		stopifnot(class(object) == "CNSet")
289 
-		createIntermediateObjects <- FALSE
290 
-	} else {
291 
-		createIntermediateObjects <- TRUE
292 
-		## 33G for 1239 files
293 
-		cnOptions[["save.it"]] <- TRUE
294 
-		##crlmmResults <- crlmmWrapper(filenames, cnOptions, ...)
295 
-		crlmmWrapper(filenames, cnOptions, ...)
296 
-	}
297 
-	verbose <- cnOptions[["verbose"]]
298 
-	load.it <- cnOptions[["load.it"]]
299 
-	outdir <- cnOptions[["outdir"]]
300 
-	snprmaFile <- cnOptions[["snprmaFile"]]
301 
-	cnFile <- cnOptions[["cnFile"]]
302 
-	cnrmaFile <- cnOptions[["cnrmaFile"]]
303 
-	snprmaFile <- cnOptions[["snprmaFile"]]
304 
-	callsFile <- cnOptions[["callsFile"]]
305 
-	confsFile <- cnOptions[["confsFile"]]
306 
-	AFile <- cnOptions[["AFile"]]
307 
-	BFile <- cnOptions[["BFile"]]
308 
-	CAFile <- cnOptions[["CAFile"]]
309 
-	CBFile <- cnOptions[["CBFile"]]
310 
-	path <- system.file("extdata", package=paste(cnOptions[["cdfName"]], "Crlmm", sep=""))
311 
-	load(file.path(path, "snpProbes.rda"))
312 
-	snpProbes <- get("snpProbes")
313 
-	load(file.path(path, "cnProbes.rda"))
314 
-	cnProbes <- get("cnProbes")
315 
-	k <- grep("chr", colnames(snpProbes))
316 
-	if(verbose) message("Loading quantile-normalized intensities...")
317 
-	##cwd <- getwd()
318 
-	##setwd(dirname(snprmaFile[1]))
319 
-	load(snprmaFile)
320 
-	res <- get("res")
321 
-	load(AFile)
322 
-	if(isPackageLoaded("ff")) open(A)
323 
-	load(BFile)
324 
-	if(isPackageLoaded("ff")) open(B)
325 
-	message("Loading genotype calls...")
326 
-	load(callsFile)
327 
-	calls <- get("calls")
328 
-	if(isPackageLoaded("ff")) open(calls)
329 
-	load(confsFile)
330 
-	confs <- get("confs")
331 
-	if(isPackageLoaded("ff")) open(confs)
332 
-	##fns <- rownames(A)
333 
-	fns <- c(res[["gns"]], res[["cnnames"]])
334 
-	if(length(fns) != nrow(A)) stop("check featurenames. fns should be the rownames of A")
335 
-	nr <- nrow(A); nc <- ncol(A)
336 
-	if(isPackageLoaded("ff")){
337 
-		if(file.exists(CAFile)){
338 
-			load(CAFile)
339 
-			if(is.null(dim(CA)) | !all(dim(CA) == dim(A))) {
340 
-				unlink(CAFile)
341 
-				CA <- initializeBigMatrix(nr, nc)
342 
-			}
343 
-		} else CA <- initializeBigMatrix(nr, nc)
344 
-		if(file.exists(CBFile)){
345 
-			load(CBFile)
346 
-			if(is.null(dim(CB)) | !all(dim(CB) == dim(A))) {
347 
-				CB <- initializeBigMatrix(nr, nc)
348 
-			}
349 
-		} else CB <- initializeBigMatrix(nr, nc)
350 
-		open(CA)
351 
-		open(CB)
352 
-	}
353 
-	##cnFile <- cnOptions[["cnFile"]]
354 
-	chromosome <- cnOptions[["chromosome"]]
355 
-	SNRmin <- cnOptions[["SNRmin"]]
356 
-	ll <- 1
357 
-	scanDates <- data.frame(ScanDate=sapply(filenames, celfileDate))
358 
-	rownames(scanDates) <- basename(rownames(scanDates))
359 
-	protocoldata <- new("AnnotatedDataFrame",
360 
-			    data=scanDates,
361 
-			    varMetadata=data.frame(labelDescription=colnames(scanDates),
362 
-			    row.names=colnames(scanDates)))
363 
-	##load(file.path(cnOptions[["outdir"]], "sampleStats.rda"))
364 
-	sampleStats <- data.frame(SKW=res$SKW,
365 
-				  SNR=res$SNR,
366 
-				  mixtureParams=res$mixtureParams,
367 
-				  gender=res$gender,
368 
-				  batch=cnOptions[["batch"]])
369 
-	##sampleStats, batch=cnOptions[["batch"]])
370 
-	pD <- new("AnnotatedDataFrame",
371 
-		  data=sampleStats,
372 
-		  varMetadata=data.frame(labelDescription=colnames(sampleStats)))
373 
-	batch <- cnOptions[["batch"]]
374 
-	if(isPackageLoaded("ff")){
375 
-##		featureDataFF <- ffdf(position=ff(rep(0L, length(fns)), vmode="integer", finalizer="close"),
376 
-##				      chromosome=ff(rep(0L, length(fns)), vmode="integer", finalizer="close"),
377 
-##				      isSnp=ff(rep(0L, length(fns)), vmode="integer", finalizer="close"),
378 
-##				      row.names=fns)
379 
-##		fD <- vector("list", length(chromosome))
380 
-		featureDataFF <- ff(dim=c(nrow(A), 17*length(unique(batch))+3), vmode="double", finalizer="close",
381 
-				    overwrite=TRUE)
382 
-	}
383 
-	for(CHR in chromosome){
384 
-		snps <- rownames(snpProbes)[snpProbes[, k] == CHR]
385 
-		cns <- rownames(cnProbes)[cnProbes[, k] == CHR]
386 
-		index.snps <- match(snps, fns)
387 
-		index.cn <- match(cns, fns)
388 
-		row.index <- c(index.snps, index.cn)
389 
-		cat("Chromosome ", CHR, "\n")
390 
-		if(isPackageLoaded("ff")){
391 
-			fD.batch <- vector("list", length(unique(batch)))
392 
-		}
393 
-		for(i in seq(along=unique(batch))){
394 
-			PLATE <- unique(batch)[i]
395 
-			message("Plate: ", PLATE)
396 
-			sample.index <- which(batch==PLATE)
397 
-			##cnOptions[["batch"]] <- cnOptions[["batch"]][snpI[["SNR"]]  >= SNRmin]
398 
-			if(isPackageLoaded("ff")){
399 
-				ca <- CA[row.index, sample.index]
400 
-				cb <- CB[row.index, sample.index]
401 
-			} else{
402 
-				##dns <- dimnames(A[row.index, sample.index])
403 
-				cb <- ca <- matrix(NA, nr=length(row.index), nc=length(sample.index))##, dimnames=dns)
404 
-			}
405 
-			cnSet <- new("CNSet",
406 
-				     alleleA=A[row.index, sample.index],
407 
-				     alleleB=B[row.index, sample.index],
408 
-				     call=calls[row.index, sample.index],
409 
-				     callProbability=confs[row.index, sample.index],
410 
-				     CA=ca,
411 
-				     CB=cb,
412 
-				     featureData=annotatedDataFrameFrom(A[row.index, sample.index], byrow=TRUE),
413 
-				     phenoData=pD[sample.index, ],
414 
-				     protocolData=protocoldata[sample.index, ])
415 
-			##Verify this is correct
416 
-			annotation(cnSet) <- cnOptions[["cdfName"]]
417 
-			featureNames(cnSet) <- fns[row.index]
418 
-			##add chromosome, position, isSnp
419 
-			cnSet <- annotate(cnSet)
420 
-##			if(any(cnSet$SNR > SNRmin)){
421 
-##				if(CHR == chromosome[1]) message(paste("Excluding samples with SNR < ", SNRmin))
422 
-##				cnSet <- cnSet[, cnSet$SNR >= SNRmin]
423 
-##			}
424 
-			featureData(cnSet) <- lm.parameters(cnSet, cnOptions)
425 
-			if(CHR < 24){
426 
-				cnSet <- computeCopynumber(cnSet, cnOptions)
427 
-				if(isPackageLoaded("ff")){
428 
-					if(i == 1) {  ## first batch
429 
-						featureDataFF[row.index, 1:20] <- as.matrix(fData(cnSet))
430 
-						fcol <- 20
431 
-					} else {
432 
-						featureDataFF[row.index, (fcol+1):(fcol+17)]
433 
-						fcol <- fcol+17
434 
-						##remove redundant columns
435 
-					}
436 
-					CA[row.index, sample.index] <- cnSet@assayData[["CA"]]
437 
-					CB[row.index, sample.index] <- cnSet@assayData[["CB"]]
438 
-					next() ## next batch
439 
-				} else {
440 
-					save(cnSet, file=paste(cnFile, "_", PLATE, "_", CHR, ".rda", sep=""))
441 
-				}
442 
-			} else break()  ## break out of the batch loop.  Go to next chromosome
443 
-			##		if(length(chromosome) == 1 & length(unique(batch)) == 1){
444 
-			##			if(cnOptions[["save.cnset"]] & !isLoadedPackage("ff"))
445 
-			##				save(cnSet, file=paste(cnFile, "_", PLATE, "_", CHR, ".rda", sep=""))
446 
-			##			return(cnSet)
447 
-			##		} else {
448 
-			##			##either multiple chromosome or multiple batches...save to file if ff is not loaded
449 
-			##			if(!isPackageLoaded("ff")){
450 
-			##				save(cnSet, file=paste(cnFile, "_", PLATE, "_", CHR, ".rda", sep=""))
451 
-			##			}
452 
-			##			rm(cnSet); gc()
453 
-			##	}
454 
-		} ## end of batch loop
455 
-	} ## end of chromosome loop
456 
-	if(isPackageLoaded("ff")) {
457 
-		close(A); close(B)
458 
-		close(featureDataFF)
459 
-		close(CA); close(CB)
460 
-		save(featureDataFF, file=file.path(outdir, "featureDataFF.rda"))
461 
-		save(CA, file=CAFile)
462 
-		save(CB, file=CBFile)
463 
-		close(calls); close(confs)
464 
-		ffSet <- new("FFSet",
465 
-			     A=A,
466 
-			     B=B,
467 
-			     snpCall=calls,
468 
-			     callProbability=confs,
469 
-			     CA=CA,
470 
-			     CB=CB)
471 
-		return(ffSet)
472 
-	}
473 
-}
474 380
475 381
476 
-loadIlluminaRG <- function(rgFile, crlmmFile, load.it, save.it,...){
477 
-##	if(missing(rgFile)){
478 
-##		##stop("must specify 'rgFile'.")
479 
-##		rgFile <- file.path(dirname(crlmmFile), "rgFile.rda")
480 
-##		message("rgFile not specified.  Using ", rgFile)
382 
+##loadIlluminaRG <- function(rgFile, crlmmFile, load.it, save.it,...){
383 
+####	if(missing(rgFile)){
384 
+####		##stop("must specify 'rgFile'.")
385 
+####		rgFile <- file.path(dirname(crlmmFile), "rgFile.rda")
386 
+####		message("rgFile not specified.  Using ", rgFile)
387 
+####	}
388 
+##	if(!load.it){
389 
+##		RG <- readIdatFiles(...)
390 
+##		if(save.it) save(RG, file=rgFile)
481 391 
 ##	}
482 
-	if(!load.it){
483 
-		RG <- readIdatFiles(...)
484 
-		if(save.it) save(RG, file=rgFile)
485 
-	}
486 
-	if(load.it & !file.exists(rgFile)){
487 
-		message("load.it is TRUE, but rgFile not present.  Attempting to read the idatFiles.")
488 
-		RG <- readIdatFiles(...)
489 
-		if(save.it) save(RG, file=rgFile)
490 
-	}
491 
-	if(load.it & file.exists(rgFile)){
492 
-		message("Loading RG file")
493 
-		load(rgFile)
494 
-		RG <- get("RG")
495 
-	}
496 
-	return(RG)
497 
-}
498 
-
499 
-loadIlluminaCallSet <- function(crlmmFile, snprmaFile, RG, load.it, save.it, cdfName){
500 
-	if(!file.exists(crlmmFile) | !load.it){
501 
-		callSet <- crlmmIllumina(RG=RG,
502 
-					 cdfName=cdfName,
503 
-					 sns=sampleNames(RG),
504 
-					 returnParams=TRUE,
505 
-					 save.it=TRUE,
506 
-					 intensityFile=snprmaFile)
507 
-		if(save.it) save(callSet, file=crlmmFile)
508 
-	} else {
509 
-		message("Loading ", crlmmFile, "...")
510 
-		load(crlmmFile)
511 
-		callSet <- get("callSet")
512 
-	}
513 
-	protocolData(callSet) <- protocolData(RG)
514 
-	return(callSet)
515 
-}
392 
+##	if(load.it & !file.exists(rgFile)){
393 
+##		message("load.it is TRUE, but rgFile not present.  Attempting to read the idatFiles.")
394 
+##		RG <- readIdatFiles(...)
395 
+##		if(save.it) save(RG, file=rgFile)
396 
+##	}
397 
+##	if(load.it & file.exists(rgFile)){
398 
+##		message("Loading RG file")
399 
+##		load(rgFile)
400 
+##		RG <- get("RG")
401 
+##	}
402 
+##	return(RG)
403 
+##}
404 
+##
405 
+##loadIlluminaCallSet <- function(crlmmFile, snprmaFile, RG, load.it, save.it, cdfName){
406 
+##	if(!file.exists(crlmmFile) | !load.it){
407 
+##		callSet <- crlmmIllumina(RG=RG,
408 
+##					 cdfName=cdfName,
409 
+##					 sns=sampleNames(RG),
410 
+##					 returnParams=TRUE,
411 
+##					 save.it=TRUE,
412 
+##					 intensityFile=snprmaFile)
413 
+##		if(save.it) save(callSet, file=crlmmFile)
414 
+##	} else {
415 
+##		message("Loading ", crlmmFile, "...")
416 
+##		load(crlmmFile)
417 
+##		callSet <- get("callSet")
418 
+##	}
419 
+##	protocolData(callSet) <- protocolData(RG)
420 
+##	return(callSet)
421 
+##}
516 422
517 423
518 424 
 ##loadAffyCallSet <- function(filenames, confsFile, callsFile, snprmaFile, load.it, save.it,  cdfName){
... ... 
@@ -544,109 +450,121 @@ loadIlluminaCallSet <- function(crlmmFile, snprmaFile, RG, load.it, save.it, cdf
544 450 
 ##	return(cnrmaResult)
545 451 
 ##}
546 452
547 
-loadIlluminaCnrma <- function(){
548 
-	if(exists("cnAB")){
549 
-		np.A <- as.integer(cnAB$A)
550 
-		np.B <- as.integer(cnAB$B)
551 
-		np <- ifelse(np.A > np.B, np.A, np.B)
552 
-		np <- matrix(np, nrow(cnAB$A), ncol(cnAB$A))
553 
-		rownames(np) <- cnAB$gns
554 
-		colnames(np) <- cnAB$sns
555 
-		cnAB$NP <- np
556 
-		##sampleNames(callSet) <- res$sns
557 
-		sampleNames(callSet) <- cnAB$sns
558 
-		cnrmaResult <- get("cnAB")
559 
-	} else cnrmaResult <- NULL
560 
-	return(cnrmaResult)
561 
-}
562 
-
563 
-crlmmWrapper <- function(filenames, cnOptions, ...){
564 
-	crlmmBatchSize <- cnOptions[["crlmmBatchSize"]]
565 
-	cdfName <- cnOptions[["cdfName"]]
566 
-	load.it <- cnOptions[["load.it"]]
567 
-	save.it <- cnOptions[["save.it"]]
568 
-	callsFile <- cnOptions[["callsFile"]]
569 
-	confsFile <- cnOptions[["confsFile"]]
570 
-	AFile=cnOptions[["AFile"]]
571 
-	BFile=cnOptions[["BFile"]]
572 
-	snprmaFile=cnOptions[["snprmaFile"]]
573 
-	cnrmaFile=cnOptions[["cnrmaFile"]]
574 
-	rgFile=cnOptions[["rgFile"]]
575 
-	outdir <- cnOptions[["outdir"]]
576 
-	if(missing(cdfName)) stop("cdfName is missing -- a valid cdfName is required.  See crlmm:::validCdfNames()")
577 
-	platform <- whichPlatform(cdfName)
578 
-	if(!(platform %in% c("affymetrix", "illumina"))){
579 
-		stop("Only 'affymetrix' and 'illumina' platforms are supported at this time.")
580 
-	} else {
581 
-		message("Checking whether annotation package for the ", platform, " platform is available")
582 
-		if(!isValidCdfName(cdfName)){
583 
-			cat("FALSE\n")
584 
-			stop(cdfName, " is not a valid entry.  See crlmm:::validCdfNames(platform)")
585 
-		} else cat("TRUE\n")
586 
-	}
587 
-	if(platform == "illumina") RG <- loadIlluminaRG(rgFile, callsFile, load.it, save.it)
588 
-	if(!(file.exists(dirname(callsFile)))) stop(dirname(callsFile), " does not exist.")
589 
-	if(!(file.exists(dirname(snprmaFile)))) stop(dirname(snprmaFile), " does not exist.")
590 
-##	if(load.it){
591 
-##		if(!file.exists(callsFile)){
592 
-##			message("load.it is TRUE, but ", callsFile, " does not exist.  Rerunning the genotype calling algorithm")
593 
-##			##load.it <- FALSE
594 
-##		}
453 
+##loadIlluminaCnrma <- function(){
454 
+##	if(exists("cnAB")){
455 
+##		np.A <- as.integer(cnAB$A)
456 
+##		np.B <- as.integer(cnAB$B)
457 
+##		np <- ifelse(np.A > np.B, np.A, np.B)
458 
+##		np <- matrix(np, nrow(cnAB$A), ncol(cnAB$A))
459 
+##		rownames(np) <- cnAB$gns
460 
+##		colnames(np) <- cnAB$sns
461 
+##		cnAB$NP <- np
462 
+##		##sampleNames(callSet) <- res$sns
463 
+##		sampleNames(callSet) <- cnAB$sns
464 
+##		cnrmaResult <- get("cnAB")
465 
+##	} else cnrmaResult <- NULL
466 
+##	return(cnrmaResult)
467 
+##}
468 
+##
469 
+##crlmmWrapper <- function(filenames, cnOptions, ...){
470 
+##	crlmmBatchSize <- cnOptions[["crlmmBatchSize"]]
471 
+##	cdfName <- cnOptions[["cdfName"]]
472 
+##	load.it <- cnOptions[["load.it"]]
473 
+##	save.it <- cnOptions[["save.it"]]
474 
+##	callsFile <- cnOptions[["callsFile"]]
475 
+##	confsFile <- cnOptions[["confsFile"]]
476 
+##	AFile=cnOptions[["AFile"]]
477 
+##	BFile=cnOptions[["BFile"]]
478 
+##	snprmaFile=cnOptions[["snprmaFile"]]
479 
+##	cnrmaFile=cnOptions[["cnrmaFile"]]
480 
+##	rgFile=cnOptions[["rgFile"]]
481 
+##	protocolFile <- cnOptions[["protocolFile"]]
482 
+##	outdir <- cnOptions[["outdir"]]
483 
+##	if(missing(cdfName)) stop("cdfName is missing -- a valid cdfName is required.  See crlmm:::validCdfNames()")
484 
+##	platform <- whichPlatform(cdfName)
485 
+##	if(!(platform %in% c("affymetrix", "illumina"))){
486 
+##		stop("Only 'affymetrix' and 'illumina' platforms are supported at this time.")
487 
+##	} else {
488 
+##		if(!isValidCdfName(cdfName)){
489 
+##			stop(cdfName, " is not a valid entry.  See crlmm:::validCdfNames(platform)")
490 
+##		} else  message("Using the annotation package ", cdfName, " for this ", platform, " platform")
595 491 
 ##	}
596 
-	if(platform == "affymetrix"){
597 
-##		if(!file.exists(callsFile) | !load.it){
598 
-			crlmm(filenames=filenames,
599 
-			      cdfName=cdfName,
600 
-			      save.it=TRUE,
601 
-			      load.it=load.it,
602 
-			      snprmaFile=snprmaFile,
603 
-			      callsFile=callsFile,
604 
-			      confsFile=confsFile,
605 
-			      AFile=AFile,
606 
-			      BFile=BFile,
607 
-			      crlmmBatchSize=crlmmBatchSize)
608 
-##		}
609 
-	}
610 
-	gc()
611 
-	if(platform == "illumina") {
612 
-		browser()
613 
-		callSet <- loadIlluminaCallSet(callsFile, snprmaFile, RG, load.it, save.it, cdfName)
614 
-	}
615 
-	if(platform == "affymetrix"){
616 
-		if(!file.exists(cnrmaFile) | !load.it){
617 
-			message("Quantile normalizing the copy number probes...")
618 
-			## updates A matrix and saves cnrmaFile
619 
-			cnrma(filenames=filenames, cdfName=cdfName, outdir=outdir, cnrmaFile=cnrmaFile, AFile=AFile)
620 
-		}
621 
-	}
622 
-##	if(!is.null(cnrmaResult)){
623 
-##		for(CHR in chromosome){
624 
-##			cat(CHR, " ")
625 
-##			cnps <- rownames(cnProbes)[cnProbes[, k] == CHR]
626 
-##			index.nps <- match(cnps, rownames(cnrmaResult[["NP"]]))
627 
-##			NP <- cnrmaResult$NP[index.nps, ]
628 
-##			save(NP, file=file.path(tmpdir, paste("NP_", CHR, ".rda", sep="")))
629 
-##			rm(NP); gc()
492 
+##	if(platform == "illumina") {
493 
+##		if(!file.exists(rgFile)){
494 
+##			if(load.it) message(rgFile, " does not exist and you chose to load.it.  Re-reading the R and G intensities from the IDAT files")
495 
+##			sampleSheet <- cnOptions$sampleSheet
496 
+##			ids <- cnOptions$ids
497 
+##			arrayInfoColNames <- cnOptions$arrayInfoColNames
498 
+##			highDensity <- cnOptions$highDensity
499 
+##			##this is either an NChannelSet object, or a list of pointers to the ff objects
500 
+##			RG <- readIdatFiles(sampleSheet=sampleSheet,
501 
+##					    arrayNames=basename(filenames),
502 
+##					    ids=ids,
503 
+##					    path=dirname(filenames),
504 
+##					    highDensity=highDensity,
505 
+##					    fileExt=cnOptions$fileExt[1:2],
506 
+##					    sep=cnOptions$fileExt[[3]],
507 
+##					    saveDate=FALSE,  ## I do this earlier
508 
+##					    verbose=cnOptions[["verbose"]],
509 
+##					    protocolFile=protocolFile)
510 
+##			if(save.it) save(RG, file=rgFile)
511 
+##			##RG <- loadIlluminaRG(rgFile, callsFile, load.it, save.it)
512 
+##		} else{
513 
+##			if(!isPackageLoaded("ff")) {load(rgFile); RG <- get("RG")}
630 514 
 ##		}
631 515 
 ##	}
632 
-	if(!save.it){
633 
-		message("Cleaning up")
634 
-		unlink(snprmaFile); unlink(cnrmaFile)
635 
-	}
636 
-}
637 
-
638 
-
516 
+##	if(!(file.exists(dirname(callsFile)))) stop(dirname(callsFile), " does not exist.")
517 
+##	if(!(file.exists(dirname(snprmaFile)))) stop(dirname(snprmaFile), " does not exist.")
518 
+##	if(platform == "affymetrix"){
519 
+##		crlmm(filenames=filenames,
520 
+##		      cdfName=cdfName,
521 
+##		      save.it=TRUE,
522 
+##		      load.it=load.it,
523 
+##		      snprmaFile=snprmaFile,
524 
+##		      callsFile=callsFile,
525 
+##		      confsFile=confsFile,
526 
+##		      AFile=AFile,
527 
+##		      BFile=BFile,
528 
+##		      crlmmBatchSize=crlmmBatchSize,
529 
+##		      SNRMin=cnOptions[["SNRMin"]])
530 
+##	}
531 
+##	gc()
532 
+##	if(platform == "illumina") {
533 
+##		callSet <- crlmmIllumina(RG=RG,
534 
+##					 cdfName=cdfName,
535 
+##					 sns=sampleNames(RG),
536 
+##					 returnParams=TRUE,
537 
+##					 save.it=TRUE,
538 
+##					 snprmaFile=snprmaFile,
539 
+##					 callsFile=callsFile,
540 
+##					 confsFile=confsFile,
541 
+##					 AFile=AFile,
542 
+##					 BFile=BFile)
543 
+##		##callSet <- loadIlluminaCallSet(callsFile, snprmaFile, RG, load.it, save.it, cdfName)
544 
+##	}
545 
+##	if(platform == "affymetrix"){
546 
+##		if(!file.exists(cnrmaFile) | !load.it){
547 
+##			message("Quantile normalizing the copy number probes...")
548 
+##			## updates A matrix and saves cnrmaFile
549 
+##			cnrma(filenames=filenames, cdfName=cdfName, outdir=outdir, verbose=cnOptions[["verbose"]], cnrmaFile=cnrmaFile, AFile=AFile, snprmaFile=snprmaFile)
550 
+##		}
551 
+##	}
552 
+####	if(!is.null(cnrmaResult)){
553 
+####		for(CHR in chromosome){
554 
+####			cat(CHR, " ")
555 
+####			cnps <- rownames(cnProbes)[cnProbes[, k] == CHR]
556 
+####			index.nps <- match(cnps, rownames(cnrmaResult[["NP"]]))
557 
+####			NP <- cnrmaResult$NP[index.nps, ]
558 
+####			save(NP, file=file.path(tmpdir, paste("NP_", CHR, ".rda", sep="")))
559 
+####			rm(NP); gc()
560 
+####		}
561 
+####	}
562 
+##	if(!save.it){
563 
+##		message("Cleaning up")
564 
+##		unlink(snprmaFile); unlink(cnrmaFile)
565 
+##	}
566 
+##}
639 567
640 
-whichPlatform <- function(cdfName){
641 
-	index <- grep("genomewidesnp", cdfName)
642 
-	if(length(index) > 0){
643 
-		platform <- "affymetrix"
644 
-	} else{
645 
-		index <- grep("human", cdfName)
646 
-		platform <- "illumina"
647 
-	}
648 
-	return(platform)
649 
-}
650 568
651 569
652 570 
 # steps: quantile normalize hapmap: create 1m_reference_cn.rda object
... ... 
@@ -693,25 +611,25 @@ whichPlatform <- function(cdfName){
693 611 
 ##	return(res3)
694 612 
 ##}
695 613
696 
-cnrma <- function(filenames, cdfName, sns, seed=1, verbose=FALSE, outdir, cnrmaFile, AFile){
614 
+cnrma <- function(object, filenames){
615 
+	ops <- crlmmOptions(object)
616 
+	cdfName <- annotation(object)
617 
+	seed <- ops$seed
618 
+	verbose <- ops$verbose
619 
+	##cnrmaFile <- ops$cnrmaFile
620 
+	A <- A(object)
697 621 
 	if(missing(cdfName)) stop("must specify cdfName")
698 622 
 	pkgname <- getCrlmmAnnotationName(cdfName)
699 623 
 	require(pkgname, character.only=TRUE) || stop("Package ", pkgname, " not available")
700 
-	if (missing(sns)) sns <- basename(filenames)
624 
+	sns <- basename(filenames)
701 625 
         loader("npProbesFid.rda", .crlmmPkgEnv, pkgname)
702 626 
 	fid <- getVarInEnv("npProbesFid")
703 627 
 	set.seed(seed)
704 628 
 	idx2 <- sample(length(fid), 10^5) ##for skewness. no need to do everything
705 629 
 	SKW <- vector("numeric", length(filenames))
706 
-	load(AFile)
707 
-	if(isPackageLoaded("ff")) open(A)
708 
-	path <- system.file("extdata", package=pkgname)
709 
-	load(file.path(path, "cnProbes.rda"))
710 
-	cnProbes <- get("cnProbes")
711 
-	cnps <- rownames(cnProbes)
712 
-	cnps <- cnps[cnps %in% rownames(A)]
713 
-	index <- match(cnps, rownames(A), nomatch=0)
714 
-	index <- index[index != 0]
630 
+	index <- match(names(fid), featureNames(object))
631 
+	stopifnot(identical(featureNames(object)[index], names(fid)))
632 
+	if(length(index) < 1) stop("None of the names for the nonpolymorphic probes in the annotation package match the names stored in the snprmaFile.")
715 633 
 	if(verbose){
716 634 
 		message("Processing ", length(filenames), " files.")
717 635 
 		if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=length(filenames), style=3)
... ... 
@@ -723,26 +641,21 @@ cnrma <- function(filenames, cdfName, sns, seed=1, verbose=FALSE, outdir, cnrmaF
723 641 
 		loader("5.0_reference_cn.rda", .crlmmPkgEnv, pkgname)
724 642 
 	}
725 643 
 	reference <- getVarInEnv("reference")
726 
-	##if(!is.matrix(reference)) stop("target distribution for quantile normalization not available.")
727 644 
 	for(i in seq(along=filenames)){
728 645 
 		y <- as.matrix(read.celfile(filenames[i], intensity.means.only=TRUE)[["INTENSITY"]][["MEAN"]][fid])
729 646 
 		x <- log2(y[idx2])
730 647 
 		SKW[i] <- mean((x-mean(x))^3)/(sd(x)^3)
731 648 
 		rm(x); gc()
732 649 
 		A[index, i] <- as.integer(normalize.quantiles.use.target(y, target=reference))
733 
-		##NP[, i] <- as.integer(normalize.quantiles.use.target(y, target=reference))
734 650 
 		if (verbose)
735 651 
 			if (getRversion() > '2.7.0') setTxtProgressBar(pb, i)
736 652 
 			else cat(".")
737 653 
 		rm(y); gc()
738 654 
 	}
739 
-	message("Done")
740 
-	cnrmaResults <- list(SKW=SKW)
741 
-	save(cnrmaResults, file=cnrmaFile)
742 
-	if(isPackageLoaded("ff")) close(A)
743 
-	save(A, file=AFile)
744 
-	rm(list=ls()); gc()
745 
-	return()
655 
+	cat("\nDone\n")
656 
+	pData(object)$SKW_nonpolymorphic <- SKW
657 
+	object@assayData[["alleleA"]] <- A
658 
+	return(object)
746 659 
 }
747 660
748 661 
 getFlags <- function(object, PHI.THR){
... ... 
@@ -760,7 +673,7 @@ getFlags <- function(object, PHI.THR){
760 673 
 }
761 674
762 675
763 
-instantiateObjects <- function(object, cnOptions){
676 
+instantiateObjects <- function(object){
764 677 
 	Ns <- matrix(NA, nrow(object), 5)
765 678 
 	colnames(Ns) <- c("A", "B", "AA", "AB", "BB")
766 679 
 	vA <- vB <- muB <- muA <- Ns
... ... 
@@ -787,149 +700,38 @@ thresholdCopynumber <- function(object){
787 700 
 	return(object)
788 701 
 }
789 702
790 
-##preprocessOptions <- function(callsFile="snpsetObject.rda",
791 
-##			      snprmaFile="normalizedIntensities.rda",
792 
-##			      rgFile="rgFile.rda"){
793 
-##
794 
-##}
795 
-
796 
-cnOptions <- function(outdir="./",
797 
-		      cdfName,
798 
-		      AFile="A.rda",
799 
-		      BFile="B.rda",
800 
-		      CAFile="CA.rda",
801 
-		      CBFile="CB.rda",
802 
-		      callsFile="genotypes.rda",
803 
-		      rgFile="rgFile.rda",
804 
-		      cnFile="cnSet",
805 
-		      cnrmaFile="cn_rmaResult.rda",
806 
-		      ##npBinary="NP.bin",  ##name of file.backed.big.matrix
807 
-		      ##npDesc="NP.desc",
808 
-		      snprmaFile="snp_rmaResult.rda",
809 
-		      ##callsFile="calls.desc",
810 
-		      ##confsFile="confsFile.desc",
811 
-		      confsFile="confs.rda",
812 
-		      save.it=TRUE,
813 
-		      save.cnset=TRUE,
814 
-		      load.it=TRUE,
815 
-		      MIN.OBS=3,
816 
-		      MIN.SAMPLES=10,
817 
-		      batch=NULL,
818 
-		      DF.PRIOR=50,
819 
-		      bias.adj=FALSE,
820 
-		      prior.prob=rep(1/4, 4),
821 
-		      SNRmin=4,
822 
-		      chromosome=1:24,
823 
-		      seed=123,
824 
-		      verbose=TRUE,
825 
-		      GT.CONF.THR=0.99,
826 
-		      PHI.THR=2^6,##used in nonpolymorphic fxn for training
827 
-		      nHOM.THR=5, ##used in nonpolymorphic fxn for training
828 
-		      MIN.NU=2^3,
829 
-		      MIN.PHI=2^3,
830 
-		      THR.NU.PHI=TRUE,
831 
-		      thresholdCopynumber=TRUE,
832 
-		      unlink=TRUE,
833 
-		      use.poe=FALSE,
834 
-		      crlmmBatchSize=1000,
835 
-		      ...){
836 
-##	if(isPackageLoaded("ff")){
837 
-##		AFile=paste(AFile, "ff", sep="_")
838 
-##		BFile=paste(BFile, "ff", sep="_")
839 
-##		confsFile=paste(confsFile, "ff", sep="_")
840 
-##		callsFile=paste(callsFile, "ff", sep="_")
841 
-##		cnFile=paste(cnFile, "ff", sep="")
842 
-##	}
843 
-	if(length(batch) > 200) warning("This job may require a lot of RAM. Consider using the ff package in conjuction with crlmm, as described in the copynumber_ff vignette...")
844 
-	if(use.poe) require(metaArray)
845 
-	if(missing(cdfName)) stop("must specify cdfName")
846 
-	if(!file.exists(outdir)){
847 
-		message(outdir, " does not exist.  Trying to create it.")
848 
-		dir.create(outdir, recursive=TRUE)
849 
-	}
850 
-	stopifnot(isValidCdfName(cdfName))
851 
-##	if(hiddenMarkovModel){
852 
-##		hmmOpts <- hmmOptions(...)
853 
-##	}
854 
-##	if(missing(snprmaFile)){
855 
-##		snprmaFile <- file.path(outdir, "normalizedIntensities.rda")
856 
-##	}
857 
-	if(is.null(batch))
858 
-		stop("must specify batch -- should be the same length as the number of files")
859 
-	list(outdir=outdir,
860 
-	     cdfName=cdfName,
861 
-	     callsFile=file.path(outdir, callsFile),
862 
-	     confsFile=file.path(outdir, confsFile),
863 
-	     AFile=file.path(outdir, AFile),
864 
-	     BFile=file.path(outdir, BFile),
865 
-	     CAFile=file.path(outdir, CAFile),
866 
-	     CBFile=file.path(outdir, CBFile),
867 
-	     snprmaFile=file.path(outdir, snprmaFile),
868 
-	     cnrmaFile=file.path(outdir, cnrmaFile),
869 
-	     rgFile=file.path(outdir, rgFile),
870 
-	     cnFile=file.path(outdir, cnFile),
871 
-	     save.it=save.it,
872 
-	     save.cnset=save.cnset,
873 
-	     load.it=load.it,
874 
-	     MIN.OBS=MIN.OBS,
875 
-	     MIN.SAMPLES=MIN.SAMPLES,
876 
-	     batch=batch,
877 
-	     DF.PRIOR=DF.PRIOR,
878 
-	     GT.CONF.THR=GT.CONF.THR,
879 
-	     prior.prob=prior.prob,
880 
-	     bias.adj=bias.adj,
881 
-	     SNRmin=SNRmin,
882 
-	     chromosome=chromosome,
883 
-	     seed=seed,
884 
-	     verbose=verbose,
885 
-	     PHI.THR=PHI.THR,
886 
-	     nHOM.THR=nHOM.THR,
887 
-	     MIN.NU=MIN.NU,
888 
-	     MIN.PHI=MIN.PHI,
889 
-	     THR.NU.PHI=THR.NU.PHI,
890 
-	     thresholdCopynumber=thresholdCopynumber,
891 
-	     unlink=unlink,
892 
-	     use.poe=use.poe,
893 
-	     crlmmBatchSize=crlmmBatchSize)
894 
-##	     use.bigmemory=use.bigmemory)
895 
-##	     hiddenMarkovModel=hiddenMarkovModel,
896 
-##	     circularBinarySegmentation=circularBinarySegmentation,
897 
-##	     cbsOpts=cbsOpts,
898 
-##	     hmmOpts=hmmOpts) ##remove SnpSuperSet object
899 
-}
900 
-
901 703 
 ##linear model parameters
902 
-lm.parameters <- function(object, cnOptions){
903 
-	fD <- fData(object)
904 
-	batch <- object$batch
905 
-	uplate <- unique(batch)
906 
-	parameterNames <- c(paste("tau2A", uplate, sep="_"),
907 
-			    paste("tau2B", uplate, sep="_"),
908 
-			    paste("sig2A", uplate, sep="_"),
909 
-			    paste("sig2B", uplate, sep="_"),
910 
-			    paste("nuA", uplate, sep="_"),
911 
-			    paste("nuA.se", uplate, sep="_"),
912 
-			    paste("nuB", uplate, sep="_"),
913 
-			    paste("nuB.se", uplate, sep="_"),
914 
-			    paste("phiA", uplate, sep="_"),
915 
-			    paste("phiA.se", uplate, sep="_"),
916 
-			    paste("phiB", uplate, sep="_"),
917 
-			    paste("phiB.se", uplate, sep="_"),
918 
-			    paste("phiAX", uplate, sep="_"),
919 
-			    paste("phiBX", uplate, sep="_"),
920 
-			    paste("corr", uplate, sep="_"),
921 
-			    paste("corrA.BB", uplate, sep="_"),
922 
-			    paste("corrB.AA", uplate, sep="_"))
923 
-	pMatrix <- data.frame(matrix(numeric(0),
924 
-				     nrow(object),
925 
-				     length(parameterNames)),
926 
-				     row.names=featureNames(object))
927 
-	colnames(pMatrix) <- parameterNames
928 
-	fD2 <- cbind(fD, pMatrix)
929 
-	new("AnnotatedDataFrame", data=fD2,
930 
-	    varMetadata=data.frame(labelDescription=colnames(fD2),
931 
-	    row.names=colnames(fD2)))
932 
-}
704 
+##lm.parameters <- function(object, cnOptions){
705 
+##	fD <- fData(object)
706 
+##	batch <- object$batch
707 
+##	uplate <- unique(batch)
708 
+##	parameterNames <- c(paste("tau2A", uplate, sep="_"),
709 
+##			    paste("tau2B", uplate, sep="_"),
710 
+##			    paste("sig2A", uplate, sep="_"),
711 
+##			    paste("sig2B", uplate, sep="_"),
712 
+##			    paste("nuA", uplate, sep="_"),
713 
+##			    paste("nuA.se", uplate, sep="_"),
714 
+##			    paste("nuB", uplate, sep="_"),
715 
+##			    paste("nuB.se", uplate, sep="_"),
716 
+##			    paste("phiA", uplate, sep="_"),
717 
+##			    paste("phiA.se", uplate, sep="_"),
718 
+##			    paste("phiB", uplate, sep="_"),
719 
+##			    paste("phiB.se", uplate, sep="_"),
720 
+##			    paste("phiAX", uplate, sep="_"),
721 
+##			    paste("phiBX", uplate, sep="_"),
722 
+##			    paste("corr", uplate, sep="_"),
723 
+##			    paste("corrA.BB", uplate, sep="_"),
724 
+##			    paste("corrB.AA", uplate, sep="_"))
725 
+##	pMatrix <- data.frame(matrix(numeric(0),
726 
+##				     nrow(object),
727 
+##				     length(parameterNames)),
728 
+##				     row.names=featureNames(object))
729 
+##	colnames(pMatrix) <- parameterNames
730 
+##	fD2 <- cbind(fD, pMatrix)
731 
+##	new("AnnotatedDataFrame", data=fD2,
732 
+##	    varMetadata=data.frame(labelDescription=colnames(fD2),
733 
+##	    row.names=colnames(fD2)))
734 
+##}
933 735
934 736 
 nonpolymorphic <- function(object, cnOptions, tmp.objects){
935 737 
 	chromosome <- cnOptions[["chromosome"]]
... ... 
@@ -937,6 +739,7 @@ nonpolymorphic <- function(object, cnOptions, tmp.objects){
937 739 
 	CHR <- unique(chromosome(object))
938 740 
 	verbose <- cnOptions[["verbose"]]
939 741 
 	if(CHR != chromosome[1]) verbose <- FALSE
742 
+	if(batch != unique(cnOptions[["batch"]])[1]) verbose <- FALSE
940 743 
 	goodSnps <- function(object, PHI.THR, tmp.objects, nAA.THR, nBB.THR){
941 744 
 		Ns <- tmp.objects[["Ns"]]
942 745 
 		##Ns <- get("Ns", envir)
... ... 
@@ -1215,12 +1018,12 @@ withinGenotypeMoments <- function(object, cnOptions, tmp.objects){
1215 1018 
 	return(tmp.objects)
1216 1019 
 }
1217 1020
1218 
-
1219 1021 
 oneBatch <- function(object, cnOptions, tmp.objects){
1220 1022 
 	muA <- tmp.objects[["muA"]]
1221 1023 
 	muB <