@@ -513,5 +513,7 @@ function (which expects ff objects and supports parallel processing)

 2010-04-11 R. Scharpf committed version 1.5.48

 ** added a few .Rd files

+2010-04-16 B Carvalho committed version 1.5.49

+** cosmetics - looking for cause of memory spike

@@ -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: 1.5.48

+Version: 1.5.49

 Date: 2010-04-09

 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

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

@@ -349,7 +349,8 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   regionInfo <- getVarInEnv("regionInfo")

   params <- getVarInEnv("params")

-  ##IF gender not provide, we predict

+  ## IF gender not provide, we predict

+  ## FIXME: XIndex may be greater than ocProbesets()

   if(is.null(gender)){

     if(verbose) message("Determining gender.")

     XMedian <- apply(log2(A[XIndex,, drop=FALSE])+log2(B[XIndex,, drop=FALSE]), 2, median)/2

@@ -446,16 +447,16 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

     names(data4reg) <- c("AA", "AB", "BB")

     regParams <- cbind(  coef(lm(AA~AB*BB, data=data4reg)),

                        c(coef(lm(AB~AA+BB, data=data4reg)), 0), 

-                       coef(lm(BB~AA*AB, data=data4reg)))

+                         coef(lm(BB~AA*AB, data=data4reg)))

     rownames(regParams) <- c("intercept", "X", "Y", "XY")

     rm(data4reg)

     minN <- 3

     newparams[["centers"]][newparams[["N"]] < minN] <- NA

     Index <- setdiff(which(rowSums(is.na(newparams[["centers"]]))==1), YIndex)

-    if(verbose) cat("Filling out empty centers")

+    if(verbose) message("Filling out empty centers", appendLF=FALSE)

     for(i in Index){

-      if(verbose) if(i%%10000==0)cat(".")

+      if(verbose) if(i%%10000==0) message(".", appendLF=FALSE)

       mu <- newparams[["centers"]][i, ]

       j <- which(is.na(mu))

       newparams[["centers"]][i, j] <- c(1, mu[-j], prod(mu[-j]))%*%regParams[, j]

@@ -472,7 +473,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

     newparams[["centers"]][is.na(newparams[["centers"]])] <- params[["centers"]][is.na(newparams[["centers"]])]

     if(verbose) cat("\n")

-    if(verbose) message("Calculating and standardizing size of shift.")

+    if(verbose) message("Calculating and standardizing size of shift... ", appendLF=FALSE)

     GG <- DD <- newparams[["centers"]] - params[["centers"]]

     DD <- sweep(DD, 2, colMeans(DD[autosomeIndex, ]))

     SS <- cov(DD[autosomeIndex, ])

@@ -491,12 +492,15 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

       dev=1/sqrt( (2*pi)^3*det(SS))*exp(-0.5*dev)

     }

   }

+  if (verbose) message("OK")

   ## BC: must keep SD

   params[-2] <- newparams[-2]

-  

-  rm(newparams);gc(verbose=FALSE)  

-  if(verbose) cat("Calling", NR, "SNPs... ")

+  rm(newparams)

+  gc(verbose=FALSE)  

+

+  if(verbose) message("Calling ", NR, " SNPs... ", appendLF=FALSE)

+

   ## ###################

   ## ## MOVE TO C#######