@@ -59,6 +59,8 @@ BioC data packages

 * fixed documentation to acommodate this change

-2009-03-28 B Carvalho - committed version 1.0.63

+2009-03-28 B Carvalho - committed version 1.0.64

 * modified warning message

+

+* modified crlmm and cnrma to look for data at extdata/

@@ -1,14 +1,14 @@

 Package: crlmm

 Type: Package

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

-Version: 1.0.63

+Version: 1.0.64

 Date: 2008-12-28

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0.

 License: Artistic-2.0

 Imports: affyio, preprocessCore, utils, stats, genefilter, splines, Biobase, mvtnorm

-Suggests: hapmapsnp5, genomewidesnp5Crlmm, genomewidesnp6Crlmm (>= 1.0.1), methods, GGdata, snpMatrix

+Suggests: hapmapsnp5, genomewidesnp5Crlmm (>= 1.0.2), genomewidesnp6Crlmm (>= 1.0.2), methods, GGdata, snpMatrix

 Collate: AllClasses.R

          methods-SnpSet.R

 	 cnrma-functions.R

@@ -128,7 +128,8 @@ cnrma <- function(filenames, sns, cdfName, seed=1, verbose=FALSE){

 	require(pkgname, character.only=TRUE) || stop("Package ", pkgname, " not available")

 	if (missing(sns)) sns <- basename(filenames)

 	## Loading data in .crlmmPkgEnv and extracting from there

-	data("npProbesFid", package=pkgname, envir=.crlmmPkgEnv)

+        loader("npProbesFid.rda", .crlmmPkgEnv, pkgname)

+##	data("npProbesFid", package=pkgname, envir=.crlmmPkgEnv)

 	fid <- getVarInEnv("npProbesFid")

 	gc()

 	set.seed(seed)

@@ -141,7 +142,8 @@ cnrma <- function(filenames, sns, cdfName, seed=1, verbose=FALSE){

 		if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=length(filenames), style=3)

 	}

 	##load reference distribution obtained from hapmap

-	data(list="1m_reference_cn", package="genomewidesnp6Crlmm", envir=.crlmmPkgEnv)

+        loader("1m_reference_cn.rda", .crlmmPkgEnv, pkgname)

+##	data(list="1m_reference_cn", package="genomewidesnp6Crlmm", envir=.crlmmPkgEnv)

 	reference <- getVarInEnv("reference")

 	for(i in seq(along=filenames)){

 		y <- as.matrix(read.celfile(filenames[i], intensity.means.only=TRUE)[["INTENSITY"]][["MEAN"]][fid])

@@ -186,11 +188,14 @@ goodSnps <- function(phi.thr, envir, fewAA=20, fewBB=20){

 }

 instantiateObjects <- function(calls, NP, plate, envir, chrom, A, B,

-			       gender, SNRmin=5, SNR){

+			       gender, SNRmin=5, SNR,

+                               pkgname="genomewidesnp6Crlmm"){

 	envir[["chrom"]] <- chrom

 	CHR_INDEX <- paste(chrom, "index", sep="")

-	data(list=CHR_INDEX, package="genomewidesnp6Crlmm")

-        ## Rob, where does 'index[[1]]' come from?

+        fname <- paste(CHR_INDEX, ".rda", sep="")

+        loader(fname, .crlmmPkgEnv, pkgname)

+        index <- get("index", envir=.crlmmPkgEnv)

+##	data(list=CHR_INDEX, package="genomewidesnp6Crlmm")

 	A <- A[index[[1]], SNR > SNRmin]

 	B <- B[index[[1]], SNR > SNRmin]

 	calls <- calls[index[[1]], SNR > SNRmin]

@@ -388,7 +393,7 @@ computeCopynumber <- function(chrom,

 	}

 }

-nonpolymorphic <- function(plateIndex, NP, envir, CONF.THR=0.99, DF.PRIOR=50){

+nonpolymorphic <- function(plateIndex, NP, envir, CONF.THR=0.99, DF.PRIOR=50, pkgname="genomewidesnp6Crlmm"){

 	p <- plateIndex

 	CHR <- envir[["chrom"]]

 	plate <- envir[["plate"]]

@@ -446,7 +451,9 @@ nonpolymorphic <- function(plateIndex, NP, envir, CONF.THR=0.99, DF.PRIOR=50){

 	##calculate R2

 	if(CHR == 23){

 		cnvs <- envir[["cnvs"]]

-		data(cnProbes, package="genomewidesnp6Crlmm")

+                loader("cnProbes", pkgname, .crlmmPkgEnv)

+                cnProbes <- get("cnProbes", envir=.crlmmPkgEnv)

+##		data(cnProbes, package="genomewidesnp6Crlmm")

 		cnProbes <- cnProbes[match(cnvs, rownames(cnProbes)), ]

 		par <- cnProbes[, "position"] < 2709520 | (cnProbes[, "position"] > 154584237 & cnProbes[, "position"] < 154913754)

 		gender <- envir[["gender"]]

@@ -70,7 +70,9 @@ crlmmGT <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   }

   if(verbose) message("Loading annotations.")

-  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

+  loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+##  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

   ## this is toget rid of the 'no visible binding' notes

   ## variable definitions

@@ -396,9 +398,12 @@ crlmmGTTNoN <- function(A, B, SNR, mixtureParams, cdfName,

   NC <- ncol(A)

   NR <- nrow(A)

+  pkgname <- getCrlmmAnnotationName(cdfName)

   if(verbose) message("Loading annotations.")

-  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

+  loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+##  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

   ## this is toget rid of the 'no visible binding' notes

   ## variable definitions

@@ -559,9 +564,12 @@ crlmmGTNormalNoN <- function(A, B, SNR, mixtureParams, cdfName,

   NC <- ncol(A)

   NR <- nrow(A)

-  

+  pkgname <- getCrlmmAnnotationName(cdfName)

+

   if(verbose) message("Loading annotations.")

-  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

+  loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+##  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

   ## this is toget rid of the 'no visible binding' notes

   ## variable definitions

@@ -736,7 +744,9 @@ crlmmGTnm <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   }

   if(verbose) message("Loading annotations.")

-  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

+  loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+##  data(genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

   ## this is toget rid of the 'no visible binding' notes

   ## variable definitions

@@ -14,7 +14,10 @@ snprma <- function(filenames, mixtureSampleSize=10^5, fitMixture=FALSE, eps=0.1,

   }

   if(verbose) message("Loading annotations and mixture model parameters.")

-  data(preprocStuff, genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

+  loader("preprocStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("genotypeStuff.rda", .crlmmPkgEnv, pkgname)

+  loader("mixtureStuff.rda", .crlmmPkgEnv, pkgname)

+##  data(preprocStuff, genotypeStuff, mixtureStuff, package=pkgname, envir=.crlmmPkgEnv)

   autosomeIndex <- getVarInEnv("autosomeIndex")

   pnsa <- getVarInEnv("pnsa")

   pnsb <- getVarInEnv("pnsb")

@@ -134,3 +134,13 @@ list2SnpSet <- function(x, returnParams=FALSE){

         data=fd, varMetadata=fdv),

       annotation=x[["pkgname"]])

 }

+

+loader <- function(theFile, envir, pkgname){

+  stopifnot(theFile %in% c("genotypeStuff.rda", "mixtureStuff.rda", "preprocStuff.rda"))

+  theFile <- file.path(system.file(package=pkgname),

+                       "extdata", theFile)

+  if (!file.exists(theFile))

+    stop("File", theFile, "does not exist in", pkgname)

+  load(theFile, envir=envir)

+}

+

@@ -1,9 +1,5 @@

 \name{crlmm}

 \alias{crlmm}

-\alias{calls}

-\alias{calls,SnpSet-method}

-\alias{confs}

-\alias{confs,SnpSet-method}

 \title{Genotype oligonucleotide arrays with CRLMM}

 \description{

@@ -18,12 +14,9 @@ crlmm(filenames, row.names=TRUE, col.names=TRUE,

       intensityFile, mixtureSampleSize=10^5,

       eps=0.1, verbose=TRUE, cdfName, sns, recallMin=10,

       recallRegMin=1000, returnParams=FALSE, badSNP=0.7)

-calls(x)

-confs(x)

 }

 \arguments{

-  \item{x}{'SnpSet' object. Usually the result of crlmm.}

   \item{filenames}{'character' vector with CEL files to be genotyped.}

   \item{row.names}{'logical'. Use rownames - SNP names?}

   \item{col.names}{'logical'. Use colnames - Sample names?}

@@ -73,9 +66,7 @@ if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){

   ## the filenames with full path...

   ## very useful when genotyping samples not in the working directory

   cels <- list.celfiles(path, full.names=TRUE)

-  crlmmOutput <- crlmm(cels)

-  (calls(crlmmOutput)[1:10, 1:2])

-  (confs(crlmmOutput)[1:10, 1:2])

+  (crlmmOutput <- crlmm(cels))

 }

 }

 \keyword{classif}

new file mode 100644

@@ -0,0 +1,38 @@

+\name{calls}

+\alias{calls}

+\alias{calls,SnpSet-method}

+\alias{confs}

+\alias{confs,SnpSet-method}

+\title{Accessors for Calls and Confidences on a SnpSet object}

+\description{

+  \code{calls} returns the genotype calls. CRLMM stores genotype calls

+  as integers (1 - AA; 2 - AB; 3 - BB).

+

+  \code{confs} returns the confidences associated to the genotype

+  calls. THe current implementation of CRLMM stores the confidences as

+  integers by using the transformation:

+

+  conf = round(-1000*log2(1-p)),

+

+  where 'p' is the posterior probability of the call.

+}

+\usage{

+calls(x)

+confs(x)

+}

+\arguments{

+  \item{x}{SnpSet object}

+}

+\value{

+  Matrix of genotype calls or confidences.

+  }

+\examples{

+  set.seed(1)

+  theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)

+  p <- matrix(runif(20), nc=2)

+  theConfs <- round(-1000*log2(1-p))

+  obj <- new("SnpSet", call=theCalls, callProbability=theConfs)

+  calls(obj)

+  confs(obj)

+}

+\keyword{manip}