@@ -1,6 +1,6 @@

 Package: limma

-Version: 2.9.6

-Date: 2006/12/19

+Version: 2.9.7

+Date: 2006/12/30

 Title: Linear Models for Microarray Data

 Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy and Francois Pepin.

 Maintainer: Gordon Smyth <[email protected]>

@@ -1,5 +1,6 @@

 .onLoad <- function(lib, pkg) require(methods)

+#  All functions exported other than those starting with "."

 exportPattern("^[^\\.]")

 #importClassesFrom(Biobase,exprSet)

@@ -1,9 +1,9 @@

-read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...) {

+read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...) {

 #	Extracts an RG list from a series of Imagene analysis output files.

 #	Imagene requires special treatment because red and green channel

 #	intensities are in different files.

 #	Gordon Smyth

-#	14 Aug 2003.  Last modified 29 July 2006.

+#	14 Aug 2003.  Last modified 30 Dec 2006.

 	if(is.null(dim(files))) {

 		if(length(files)%%2==0)

@@ -39,11 +39,28 @@ read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun

 	}

 	if(is.null(columns$f) || is.null(columns$b)) stop("'columns' should have components 'f' and 'b'")

-#	Now read data

+#	Initialize data object

 	Y <- matrix(0,nspots,narrays)

 	colnames(Y) <- names

-	RG <- list(R=Y,G=Y,Rb=Y,Gb=Y,Image.Program="ImaGene",Field.Dimensions=FD)

+	RG <- list(R=Y,G=Y,Rb=Y,Gb=Y,source="imagene",Field.Dimensions=FD)

 	if(!is.null(wt.fun)) RG$weights <- Y

+

+#	Other columns

+	if(!is.null(other.columns)) {

+		other.columns <- as.character(other.columns)

+		if(length(other.columns)) {

+			RG$other <- list()

+			G.other.columns <- paste("G",other.columns)

+			colnames(Y) <- removeExt(files[,1])

+			for (a in G.other.columns) RG$other[[a]] <- Y 

+			R.other.columns <- paste("R",other.columns)

+			colnames(Y) <- removeExt(files[,2])

+			for (a in R.other.columns) RG$other[[a]] <- Y 

+		} else {

+			other.columns <- NULL

+		}

+	}

+

 	printer <- list(ngrid.r=FD[1,"Metarows"],ngrid.c=FD[1,"Metacols"],nspot.r=FD[1,"Rows"],nspot.c=FD[1,"Cols"])

 	if(nrow(FD)==1) {

 		RG$printer <- printer

@@ -53,7 +70,11 @@ read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun

 			all(printer$nspot.r==FD[,"Rows"]) &&

 			all(printer$nspot.c==FD[,"Cols"]) ) RG$printer <- printer

 	}

+

+#	Now read data

 	for (i in 1:narrays) {

+

+#		Green channel

 		fullname <- files[i,1]

 		if(!is.null(path)) fullname <- file.path(path,fullname)

 		if(i > 1) {

@@ -67,6 +88,11 @@ read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun

 		if(i==1) RG$genes <- obj[,c("Field","Meta Row","Meta Column","Row","Column","Gene ID")]

 		RG$G[,i] <- obj[,columns$f]

 		RG$Gb[,i] <- obj[,columns$b]

+		if(!is.null(other.columns)) {

+			for (j in 1:length(other.columns)) RG$other[[G.other.columns[j]]][,i] <- obj[,other.columns[j]]

+		}

+

+#		Red channel		

 		fullname <- files[i,2]

 		if(!is.null(path)) fullname <- file.path(path,fullname)

 		obj<- read.table(fullname,skip=skip,header=TRUE,sep=sep,quote=quote,check.names=FALSE,comment.char="",fill=TRUE,nrows=nspots,...)

@@ -74,6 +100,9 @@ read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun

 		RG$R[,i] <- obj[,columns$f]

 		RG$Rb[,i] <- obj[,columns$b]

 		if(!is.null(wt.fun)) RG$weights[,i] <- wt.fun(obj)

+		if(!is.null(other.columns)) {

+			for (j in 1:length(other.columns)) RG$other[[R.other.columns[j]]][,i] <- obj[,other.columns[j]]

+		}

 	}

 	new("RGList",RG)

 }

@@ -32,7 +32,7 @@ read.maimages <- function(files=NULL,source="generic",path=NULL,ext=NULL,names=N

 #	source2 is the source type with qualifications removed

 	source2 <- strsplit(source,split=".",fixed=TRUE)[[1]][1]

 	if(is.null(quote)) if(source=="agilent") quote <- "" else quote <- "\""

-	if(source2=="imagene") return(read.imagene(files=files,path=path,ext=ext,names=names,columns=columns,wt.fun=wt.fun,verbose=verbose,sep=sep,quote=quote,...))

+	if(source2=="imagene") return(read.imagene(files=files,path=path,ext=ext,names=names,columns=columns,other.columns=other.columns,wt.fun=wt.fun,verbose=verbose,sep=sep,quote=quote,...))

 	if(is.data.frame(files)) {

 		targets <- files

@@ -241,7 +241,7 @@ read.maimages <- function(files=NULL,source="generic",path=NULL,ext=NULL,names=N

 	new("RGList",RG)

 }

-wtVariables <- function(x,fun)

+namesInFun <- function(x,fun)

 #	Finds variable names in user-defined functions

 #	Gordon Smyth

 #	3 Nov 2004. Last modified 2 Jan 2006.

@@ -258,7 +258,7 @@ wtVariables <- function(x,fun)

 getColClasses <- function(cols, ...)

 #	Construct a colClasses vector for read.table from a vector of possible columns 'cols' 

-#	Uses wtVariables and ellipsis vectors and lists of character string variable names

+#	Uses namesInFun and ellipsis vectors and lists of character string variable names

 #	to match against 'cols'

 #	Marcus Davy 

 #	16 Nov 2004. Last revised 2 Jan 2006.

@@ -269,7 +269,7 @@ getColClasses <- function(cols, ...)

 	wanted <- list(...)

 	for(i in 1:length(wanted)) {

 		if(is.null(wanted[[i]])) next

-		if(is.function(wanted[[i]])) include <- wtVariables(cols, wanted[[i]])

+		if(is.function(wanted[[i]])) include <- namesInFun(cols, wanted[[i]])

 		if(is.list(wanted[[i]])) wanted[[i]] <- unlist(wanted[[i]])

 		if(is.character(wanted[[i]])) include <- wanted[[i]]

 		ind <- match(include, cols, nomatch=0)

@@ -277,3 +277,4 @@ getColClasses <- function(cols, ...)

 	}

 	x

 }

+

@@ -249,6 +249,7 @@ read.matrix <- function(file,nrows=0,skip=0,...) {

 #	Gordon Smyth

 #	9 Mar 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	h <- scan(file,what="character",skip=skip,nlines=1,quote="\"",quiet=TRUE,...)

 	x <- matrix(scan(file,skip=skip+1,nlines=nrows,quiet=TRUE,...),byrow=TRUE,ncol=length(h))

 	colnames(x) <- h

@@ -260,6 +261,7 @@ rg.series.spot <- function(slides,path=NULL,names.slides=names(slides),suffix="s

 #	Gordon Smyth

 #	1 Nov 2002.  Last revised 23 Mar 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	slides <- as.vector(as.character(slides))

 	if(is.null(names.slides)) names.slides <- slides

 	nslides <- length(slides)

@@ -299,6 +301,7 @@ read.series <- function(slides,path=NULL,suffix="spot",...) {

 #	Gordon Smyth

 #	11 Mar 2002.  Last revised 2 Mar 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	slides <- as.vector(as.character(slides))

 	nslides <- length(slides)

 	for (i in 1:nslides) {

@@ -318,6 +321,7 @@ m.spot <- function(spot) {

 #	Gordon Smyth

 #	18 Nov 2001.  Last revised 2 Mar 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	R <- spot[,"Rmean"] - spot[,"morphR"]

 	G <- spot[,"Gmean"] - spot[,"morphG"]

 	log(R,2) - log(G,2)

@@ -328,6 +332,7 @@ a.spot <- function(spot) {

 #	Gordon Smyth

 #	18 Nov 2001.  Last revised 2 Mar 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	R <- spot[,"Rmean"] - spot[,"morphR"]

 	G <- spot[,"Gmean"] - spot[,"morphG"]

 	(log(R,2) + log(G,2))/2

@@ -338,6 +343,7 @@ rg.spot <- function(slides,names.slides=names(slides),suffix="spot",area=FALSE)

 #	Gordon Smyth

 #	17 Jan 2002. Last revised 1 Nov 2002.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	slides <- as.vector(as.character(slides))

 	if(is.null(names.slides)) names.slides <- slides

 	nslides <- length(slides)

@@ -362,6 +368,7 @@ rg.quantarray <- function(slides,names.slides=names(slides),suffix="qta") {

 #	Gordon Smyth

 #	23 July 2002

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	slides <- as.vector(as.character(slides))

 	if(is.null(names.slides)) names.slides <- slides

 	nslides <- length(slides)

@@ -384,6 +391,7 @@ rg.genepix <- function(slides,names.slides=names(slides),suffix="gpr") {

 #	Gordon Smyth

 #	23 July 2002. Last revised 13 Feb 2003.

+	.Deprecated("read.maimages")  # 31 Dec 2006

 	slides <- as.vector(as.character(slides))

 	if(is.null(names.slides)) names.slides <- slides

 	nslides <- length(slides)

@@ -1,3 +1,11 @@

+1 Jan 2007: limma 2.9.7

+

+- old functions designed to read image data files into data.frames

+  are now deprecated. This affects functions: read.matrix, rg.series.spot,

+  read.series, m.spot, a.spot, rg.spot, rg.quantarray, rg.genepix.

+- wtVariables() renamed to namesInFun()

+- new argument other.columns for read.imagene()

+

 19 Dec 2006: limma 2.9.6

 - new function as.matrix.ExpressionSet

@@ -4,6 +4,8 @@

 \title{Extract M or A-values from SPOT data.frame or matrix}

 \description{

 Extract M-values or A-values from a SPOT data.frame or matrix.

+

+These functions are deprecated in limma 2.9.7, 1 January 2007.

 }

 \usage{

 m.spot(spot)

new file mode 100644

@@ -0,0 +1,36 @@

+\name{namesInFun}

+\alias{namesInFun}

+\title{Find names in a function definition}

+\description{

+Given a list of names, detect whether these names appear in the definition of a function.

+}	 

+\usage{

+namesInFun(x, fun)

+}

+\arguments{

+ \item{x}{A character vector of names}

+ \item{fun}{A function}

+}

+\details{

+This function is used by \code{read.maimages} as part of determining which columns needs to be read from the data file.

+It is used to find detect which of the column headings in the data file appear in the definition of the weight function specified by \code{wt.fun}.

+}

+

+\value{

+Character of vector of names found in the definition of \code{fun}

+}

+\author{Gordon Smyth}

+\seealso{

+\code{\link{getColClasses}}

+\code{\link{read.maimages}}

+

+An overview of limma read functions is given in \link{03.ReadingData}.

+}

+\examples{

+searchcols <- c("area","Flags","Ignore Filter")

+namesInFun(searchcols, wtarea)

+namesInFun(searchcols, wtflags)

+namesInFun(searchcols, wtIgnore.Filter)

+rm(searchcols) # tidy up

+}

+\keyword{file}

@@ -31,8 +31,7 @@ The function is based on unpublished work by the author.

 \examples{

 library(sma)

 data(MouseArray)

-M <- m.spot(mouse1)

-A <- a.spot(mouse1)

-M <- normalizeRobustSpline(M,A,mouse.setup)

+MA <- MA.RG(mouse.data)

+normM <- normalizeRobustSpline(MA$M[,1],MA$A[,1],mouse.setup)

 }

 \keyword{models}

@@ -7,7 +7,7 @@ Reads an RGList from a series of microarray image analysis output files

 }

 \usage{

 read.maimages(files=NULL,source="generic",path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,annotation=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote=NULL,DEBUG=FALSE,\dots)

-read.imagene(files,path=NULL,ext=NULL,names=NULL,columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...)

+read.imagene(files,path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...)

 }

 \arguments{

   \item{files}{character vector giving the names of the files containing image analysis output or, for Imagene data, a character matrix of names of files.

@@ -58,12 +58,14 @@ The function \code{read.imagene} is called by \code{read.maimages} when \code{so

 It does not need to be called directly by users.

 The argument \code{other.columns} allows arbitrary columns of the image analysis output files to be preserved in the data object.

+These become matrices in the component \code{other} component.

+For ImaGene data, the other column headings with be prefixed with \code{"R "} or \code{"G "} as appropriate.

 }

 \section{Warnings}{

 All image analysis files being read are assumed to contain data for the same genelist in the same order.

 No checking is done to confirm that this is true.

-Annotation information, when it is available, is set from the first file only.

+Probe annotation information is read from the first file only.

 }

 \value{

@@ -4,6 +4,8 @@

 \description{

 Read a numeric matrix from a file assuming column headings on the first line.

 Not normally used directly by users.

+

+This function is deprecated in limma 2.9.7 (1 January 2007).

 }

 \usage{

 read.matrix(file,nrows=0,skip=0,...)

@@ -3,6 +3,8 @@

 \title{Read series of image files}

 \description{

 Read in a series of array image analysis output files as data frames.

+

+This function is deprecated in limma 2.9.7 (1 January 2007).

 }

 \usage{

 read.series(slides, path=NULL, suffix="spot", ...)

@@ -3,6 +3,8 @@

 \title{Extract RGList from data.frames Containing GenePix Data}

 \description{

 Extracts an RGList from GenePix image analysis output when the data has already been read from files into data.frames objects.

+

+This function is deprecated in limma 2.9.7 (1 January 2007).

 }

 \usage{

 rg.genepix(slides,names.slides=names(slides),suffix="gpr")

@@ -3,6 +3,8 @@

 \title{Extract RGList from data.frames Containing Quantarray Data}

 \description{

 Extracts an RGList from Quantarray image analysis output when the data has already been read from files into data.frames objects.

+

+This function is deprecated in limma 2.9.7 (1 January 2007).

 }

 \usage{

 rg.quantarray(slides,names.slides=names(slides),suffix="qta")

@@ -3,6 +3,7 @@

 \title{Read RGList from SPOT Image Analysis Output Files}

 \description{

 Extracts an RGList from a series of Spot image analysis files.

+

 This is a depreciated function.

 Use \code{\link{read.maimages}} instead.

 }

@@ -3,6 +3,8 @@

 \title{Extract RGList from data.frames Containing SPOT Data}

 \description{

 Extracts an RGList from Spot image analysis output when the data has already been read from files into data.frames objects.

+

+This function is deprecated in limma 2.9.7 (1 January 2007).

 }

 \usage{

 rg.spot(slides,names.slides=names(slides),suffix="spot",area=FALSE)

deleted file mode 100644

@@ -1,33 +0,0 @@

-\name{wtVariables}

-\alias{wtVariables}

-\title{Read RGList from Image Analysis Output Files}

-\description{

-  Extracts variable names from weight functions such as \code{wtarea}, \code{wtflags}, \code{wtIgnore.Filter} and user defined functions for fast loading in \code{read.maimages}. 

-}	 

-\usage{

-wtVariables(x, fun)

-}

-\arguments{

- \item{x}{A character vector of all columns to search against}

- \item{fun}{A weight function to search for any of the possible columns in x}

-}

-\details{

-This is an internally called function by \code{getColClasses} which constructs a colClasses vector for fast loading of only required columns in \code{read.maimages}

-}

-

-\value{

-Vector of columns required within read.maimages

-}

-\author{Gordon Smyth}

-\seealso{

-\code{\link[limma]{getColClasses}}

-\code{\link[base]{read.table}}

-}

-\examples{

-searchcols <- c("area","Flags","Ignore Filter")

-wtVariables(searchcols, wtarea)

-wtVariables(searchcols, wtflags)

-wtVariables(searchcols, wtIgnore.Filter)

-rm(searchcols) # tidy up

-}

-\keyword{file}