@@ -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: 1.11.31

+Version: 1.11.32

 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>

@@ -2741,3 +2741,61 @@ ABpanel <- function(x, y, predictRegion,

 		}

 	}

 }

+

+calculateBAFandLRR <- function(cnSet) {

+  ## Calculates B allele frequency and log2 R ratio for all snps for a given cnSet

+  ## Returns a 3-D array of size Num Of Snps x Num of Samples x 2

+  ## where result[,,1] is B allele frequency and result[,,2] is log2 R ratio

+

+  snp.index <- which(isSnp(cnSet))

+  b <- (B(cnSet))[snp.index, ]

+  a <- (A(cnSet))[snp.index, ]

+  centers<-medians(cnSet, i=snp.index, j=1:length(unique(batch(cnSet))))

+  bafAndLrr <- array(NA_integer_, dim=c(length(snp.index), length(sampleNames(cnSet)), 2), dimnames=list(featureNames(cnSet)[snp.index], sampleNames(cnSet),c("baf", "lrr")))

+

+  for (batch in unique(batch(cnSet))) {

+

+    ## get batch- and snp-specific centers

+    center.aa.x <- centers[, 1, 1, batch]

+    center.aa.y <- centers[, 2, 1, batch]

+    center.ab.x <- centers[, 1, 2, batch]

+    center.ab.y <- centers[, 2, 2, batch]

+    center.bb.x <- centers[, 1, 3, batch]

+    center.bb.y <- centers[, 2, 3, batch]

+    theta.aa <- atan2(center.aa.y, center.aa.x) * 2 / pi

+    r.aa <- center.aa.x + center.aa.y

+    theta.ab <- atan2(center.ab.y, center.ab.x) * 2 / pi

+    r.ab <- center.ab.x + center.ab.y

+    theta.bb <- atan2(center.bb.y, center.bb.x) * 2 / pi

+    r.bb <- center.bb.x + center.bb.y

+

+    index.sample <- which(batch(cnSet) %in% batch)

+    for (i in index.sample) {

+      theta <- atan2(b[, i], a[, i]) * 2 / pi

+      r <- a[, i] + b[, i]

+

+      baf <- vector(mode="numeric", length=length(theta))

+      baf[theta < theta.aa] <- 0

+      baf[theta >= theta.bb] <- 1

+      idx.ab <- which(theta >= theta.aa & theta < theta.ab)

+      baf[idx.ab] <- .5 * (theta[idx.ab] - theta.aa[idx.ab]) / (theta.ab[idx.ab] - theta.aa[idx.ab])

+      idx.bb <- which(theta >= theta.ab & theta < theta.bb)

+      baf[idx.bb] <- .5 * (theta[idx.bb] - theta.ab[idx.bb]) / (theta.bb[idx.bb] - theta.ab[idx.bb]) + .5

+      bafAndLrr[, i ,1] <- baf

+

+      r.expected <- vector(mode="numeric", length=length(r))

+      r.expected[theta < theta.aa] <- r.aa[theta < theta.aa]

+      r.expected[theta >= theta.bb] <- r.bb[theta >= theta.bb]

+

+      idx.ab <- which(theta >= theta.aa & theta < theta.ab)

+      r.expected[idx.ab] <- (theta[idx.ab] - theta.aa[idx.ab]) * (r.ab[idx.ab]-r.aa[idx.ab]) /

+        (theta.ab[idx.ab] - theta.aa[idx.ab]) + r.aa[idx.ab]

+      idx.bb <- which(theta >= theta.ab & theta < theta.bb)

+      r.expected[idx.bb] <- (theta[idx.bb] - theta.ab[idx.bb]) * (r.bb[idx.bb]-r.ab[idx.bb])/

+        (theta.bb[idx.bb] - theta.ab[idx.bb]) + r.ab[idx.bb]

+      bafAndLrr[, i, 2] <- log2(r / r.expected)

+

+    }

+  }

+  return(bafAndLrr)

+}