@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.9.28

+Version: 1.9.29

 Date: 2010-12-10

 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -1257,7 +1257,7 @@ fit.lm4 <- function(strata,

 	nuB(object)[marker.index, batch.index] <- nuB

 	phiB(object)[marker.index, batch.index] <- phiB

 	##if(is.lds) {close(object); return(TRUE)} else return(object)

-	TRUE

+	if(is.lds) {close(object); return(TRUE)} else return(object)

 }

 whichPlatform <- function(cdfName){

@@ -2026,7 +2026,8 @@ crlmmCopynumber <- function(object,

 			    MIN.PHI=2^3,

 			    THR.NU.PHI=TRUE,

 			    type=c("SNP", "NP", "X.SNP", "X.NP")){

-	stopifnot(type %in% c("SNP", "NP", "X.SNP", "X.NP"))

+	typeof <- paste(type, collapse=",")

+	stopifnot(typeof %in% c("SNP", "NP", "SNP,NP", "SNP,X.SNP", "SNP,X.NP", "SNP,NP,X.SNP", "SNP,NP,X.SNP,X.NP"))

 	if(GT.CONF.THR >= 1 | GT.CONF.THR < 0) stop("GT.CONF.THR must be in [0,1)")

 	batch <- batch(object)

 	is.snp <- isSnp(object)

@@ -2089,7 +2090,7 @@ crlmmCopynumber <- function(object,

 		marker.index <- whichMarkers(marker.type, is.snp,

 					     is.autosome, is.annotated, is.X)

 		if(length(marker.index) == 0) next()

-		object <- estimateCnParameters(object=object,

+		res <- estimateCnParameters(object=object,

 					       type=marker.type,

 					       SNRMin=SNRMin,

 					       DF.PRIOR=DF.PRIOR,

@@ -2103,6 +2104,8 @@ crlmmCopynumber <- function(object,

 					       marker.index=marker.index,

 					       is.lds=is.lds,

 					       CHR.X=CHR.X)

+		##if(!is.lds) {object <- res; rm(res); gc()}

+		##if(!is.lds) {object <- res; rm(res); gc()}

 	}

 	close(object)

 	if(is.lds) return(TRUE) else return(object)

@@ -1009,16 +1009,16 @@ getProtocolData.Illumina = function(filenames, sep="_", fileExt="Grn.idat", verb

 constructInf <- function(sampleSheet=NULL,

-			       arrayNames=NULL,

-			       path=".",

-			       arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),

-			       highDensity=FALSE,

-			       sep="_",

-			       fileExt=list(green="Grn.idat", red="Red.idat"),

-			       cdfName,

-			       verbose=FALSE,

-			       batch, #fns,

-			       saveDate=TRUE) { #, outdir="."){

+			 arrayNames=NULL,

+			 path=".",

+			 arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),

+			 highDensity=FALSE,

+			 sep="_",

+			 fileExt=list(green="Grn.idat", red="Red.idat"),

+			 cdfName,

+			 verbose=FALSE,

+			 batch, #fns,

+			 saveDate=TRUE) { #, outdir="."){

 	verbose <- FALSE

 	if(!is.null(arrayNames)) {

 		pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

@@ -127,20 +127,8 @@ crlmmCopynumber(object, MIN.SAMPLES=10, SNRMin = 5, MIN.OBS = 1,

     \code{crlmmCopynumber}.  50 or more samples per batch is preferred

     and will improve the estimates.

-	The function crlmmCopynumber uses matrices instead of ff objects

-	if the ff library is not loaded. When the ff package is loaded,

-	large data support is enabled.  Normalized intensities

-	(\code{alleleA} and \code{alleleB}), genotype calls and

-	confidence scores (\code{snpCall} and \code{snpCallProbability})

-	are stored in \code{assayData} slot.  Summary statistics for

-	each batch, including the linear model paramters for copy

-	number, are stored in the \code{batchStatistics} slot.  Both the

-	\code{assayData} and \code{batchStatistics} slot are of class

-	\code{AssayData} with elements that are ff objects (if ff

-	package is loaded) or matrices.

-

-	The functions \code{crlmmCopynumberLD} and

-	\code{crlmmCopynumber2} have been deprecated.

+    The functions \code{crlmmCopynumberLD} and

+    \code{crlmmCopynumber2} have been deprecated.

 	The argument \code{type} can be used to specify a subset of

 	markers for which the copy number estimation algorithm is run.

@@ -155,6 +143,9 @@ crlmmCopynumber(object, MIN.SAMPLES=10, SNRMin = 5, MIN.OBS = 1,

 	'X.NP' refers to autosomes on chromosome X.

+	However, users must run 'SNP' prior to running 'NP' and 'X.NP',

+	or specify \code{type = c('SNP', 'X.NP')}.

+

       }

       \value{

@@ -162,7 +153,10 @@ crlmmCopynumber(object, MIN.SAMPLES=10, SNRMin = 5, MIN.OBS = 1,

 	The value returned by the \code{crlmmCopynumber} function

 	depends on whether the data is stored in RAM or whether the data

 	is stored on disk using the R package \code{ff} for reading /

-	writing.  Specifically,

+	writing.  If uncertain, the first line of the \code{show} method

+	defined for \code{CNSet} objects prints whether the

+	\code{assayData} elements are derived from the \code{ff} package

+	in the first line.  Specifically,

 	- if the elements of the \code{batchStaticts} slot in the

 	\code{CNSet} object have the class "ff_matrix" or "ffdf", then

@@ -177,6 +171,5 @@ crlmmCopynumber(object, MIN.SAMPLES=10, SNRMin = 5, MIN.OBS = 1,

       }

-

 \author{R. Scharpf}

 \keyword{manip}