@@ -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: 1.11.58

+Version: 1.11.60

 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>

@@ -35,8 +35,7 @@ data(cnSetExample2)

       data(hapmapSet, package="CnvScripts")

       marker.index <- which(chromosome(hapmapSet) == 8)

       marker.index <- marker.index[1:60e3]

-      sample.CNSet <- hapmapSet[marker.index, c(1168:1169)]

-      cnSetExample <- sample.CNSet

+      cnSetExample <- hapmapSet[marker.index, c(1168:1169)]

       save(cnSetExample, file="~/Software/crlmm/data/cnSetExample.rda")

       ## 2 samples, many markers

@@ -44,11 +43,10 @@ data(cnSetExample2)

       snp.index <- which(isSnp(hapmapSet))[1:100]

       np.index <- which(!isSnp(hapmapSet))[1:100]

       marker.index <- c(snp.index, np.index)

-      sample.CNSet2 <- hapmapSet[marker.index, ]

-      sample.CNSet2$gender <- sample.CNSet2$gender[]

-      sample.CNSet2$SKW <- sample.CNSet2$SKW[]

-      sample.CNSet2$SNR <- sample.CNSet2$SNR[]

-      cnSetExample2 <- sample.CNSet2

+      cnSetExample2 <- hapmapSet[marker.index, ]

+      cnSetExample2$gender <- cnSetExample2$gender[]

+      cnSetExample2$SKW <- cnSetExample2$SKW[]

+      cnSetExample2$SNR <- cnSetExample2$SNR[]

       save(cnSetExample2, file="~/Software/crlmm/data/cnSetExample2.rda")

 }

 }

@@ -99,41 +99,7 @@ if (require(genomewidesnp6Crlmm) & require(hapmapsnp6)){

   gender <- c("female", "female", "male")

   gender[gender == "female"] <- 2

   gender[gender == "male"] <- 1

-  \dontrun{

-	  ## we need the A and B intensities

-     if(require("ff")){

-	  path <- system.file("celFiles", package="hapmapsnp6")

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

-	  gtSet <- genotype(cels, batch=rep(1L,3))

-          gt1 <- calls(crlmmOutput)

-          gt2 <- calls(gtSet)[isSnp(gtSet), ]

-          gt2 <- gt2[match(rownames(gt2), rownames(gt1)), ]

-	  stopifnot(all.equal(gt1, gt2))

-

-	  XIndex <- which(chromosome(gtSet)==23 & isSnp(gtSet))

-	  YIndex <- which(chromosome(gtSet)==24 & isSnp(gtSet))

-	  A.X <- log2(A(gtSet)[XIndex,,drop=FALSE])

-	  B.X <- log2(B(gtSet)[XIndex,,drop=FALSE])

-	  meds.X <- apply(A.X+B.X, 2, median)/2

-	  A.Y <- log2(A(gtSet)[YIndex,,drop=FALSE])

-	  B.Y <- log2(B(gtSet)[YIndex,,drop=FALSE])

-	  meds.Y <- apply(A.Y+B.Y, 2, median)/2

-	  R <- meds.X - meds.Y

-	  SNR <- gtSet$SNR[]

-	  SNRMin <- 5

-	  gender <- kmeans(R, c(min(R[SNR[]>SNRMin]), max(R[SNR[]>SNRMin])))[["cluster"]]

-	  plot(seq_along(R), R, pch=21, bg=c("royalblue", "red")[gender],

-	       xlim=c(0, 4), xaxt='n', xlab="sample index")

-	  legend("topright", fill=c("royalblue", "red"), legend=c("male", "female"))

-	  delete(A(gtSet))

-	  delete(B(gtSet))

-	  delete(calls(gtSet))

-	  delete(assayDataElement(gtSet, "snpCallProbability"))

-	  ff.filenames <- list.files(".", pattern=".ff")

-	  unlink(ff.filename)

-     } ## end if(require("ff"))

-  }

 }

 \dontrun{

@@ -108,6 +108,45 @@ if (require(ff) & require(genomewidesnp6Crlmm) & require(hapmapsnp6)){

   gender[gender == "male"] <- 1

   dim(cnSet)

   table(isSnp(cnSet))

+  \dontrun{

+          ##---------------------------------------------------------------------------

+          ##

+	  ## Genotype Imputation

+          ##

+          ##---------------------------------------------------------------------------

+     if(require("ff")){

+	  path <- system.file("celFiles", package="hapmapsnp6")

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

+	  gtSet <- genotype(cels, batch=rep(1L,3))

+

+          gt1 <- calls(crlmmOutput)

+          gt2 <- calls(gtSet)[isSnp(gtSet), ]

+          gt2 <- gt2[match(rownames(gt2), rownames(gt1)), ]

+	  stopifnot(all.equal(gt1, gt2))

+

+	  XIndex <- which(chromosome(gtSet)==23 & isSnp(gtSet))

+	  YIndex <- which(chromosome(gtSet)==24 & isSnp(gtSet))

+	  A.X <- log2(A(gtSet)[XIndex,,drop=FALSE])

+	  B.X <- log2(B(gtSet)[XIndex,,drop=FALSE])

+	  meds.X <- apply(A.X+B.X, 2, median)/2

+	  A.Y <- log2(A(gtSet)[YIndex,,drop=FALSE])

+	  B.Y <- log2(B(gtSet)[YIndex,,drop=FALSE])

+	  meds.Y <- apply(A.Y+B.Y, 2, median)/2

+	  R <- meds.X - meds.Y

+	  SNR <- gtSet$SNR[]

+	  SNRMin <- 5

+	  gender <- kmeans(R, c(min(R[SNR[]>SNRMin]), max(R[SNR[]>SNRMin])))[["cluster"]]

+	  plot(seq_along(R), R, pch=21, bg=c("royalblue", "red")[gender],

+	       xlim=c(0, 4), xaxt='n', xlab="sample index")

+	  legend("topright", fill=c("royalblue", "red"), legend=c("male", "female"))

+	  delete(A(gtSet))

+	  delete(B(gtSet))

+	  delete(calls(gtSet))

+	  delete(assayDataElement(gtSet, "snpCallProbability"))

+	  ff.filenames <- list.files(".", pattern=".ff")

+	  unlink(ff.filename)

+     } ## end if(require("ff"))

+  }

 }

 }

 \keyword{ classif }