@@ -23,3 +23,8 @@ BioC data packages

 * Added biocViews

 * Removed empty \details{} in cnrma.Rd

+

+2009-03-14 Benilton Carvalho <bcarvalh@jhsph.edu> - committed version 1.0.56

+

+* Loaded data in cnrma-functions.R to an environment and extracted from there

+  so we can get rid of the NOTES complaining about 'no visible bindings'.

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

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

-Version: 1.0.55

+Version: 1.0.56

 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>

@@ -91,10 +91,16 @@ celDatesFrom <- function(celfiles, path=""){

 }

 cnrma <- function(filenames, sns, cdfName, seed=1, verbose=FALSE){

-	require(genomewidesnp6Crlmm) || stop("Package genomewidesnp6Crlmm not available")

+  ## BC: 03/14/09

+  ## getting pkgname from cdfName, in the future this might be useful

+  ## as the method might be implemented for other platforms

+  pkgname <- getCrlmmAnnotationName(cdfName)

+

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

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

-	data("npProbesFid", package="genomewidesnp6Crlmm")

-	fid <- npProbesFid

+  ## Loading data in .crlmmPkgEnv and extracting from there

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

+	fid <- getVarInEnv("npProbesFid")

 	gc()

 	set.seed(seed)

 	idx2 <- sample(length(fid), 10^5) ##for skewness. no need to do everything

@@ -106,7 +112,8 @@ 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")

+	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])

 		x <- log2(y[idx2])

@@ -893,10 +900,14 @@ coefs <- function(plateIndex, conf, MIN.OBS=3, envir, CONF.THR=0.99){

 	is.complete <- rowSums(is.na(W)) == 0

 	##is.complete <- is.complete & correct.orderA & correct.orderB & confInd & notmissing

 	nuphiAllele(allele="A", Ystar=Ystar[is.complete, ], W=W[is.complete, ], envir=envir, p=p)

-	nuA[is.complete, p] <- nu

-	phiA[is.complete, p] <- phi

-	nuA.se[is.complete, p] <- nu.se

-	phiA.se[is.complete, p] <- phi.se

+        ## ROB: can you please double check that my fix is okay?

+        ## ROB: the parameters nu/phi/nu.se/phi.se aren't defined

+        ## ROB: in this particular function. So I assume they come

+        ## ROB: from the nuphiAllele function above.

+	nuA[is.complete, p] <- get("nu", envir=envir)

+	phiA[is.complete, p] <- get("phi", envir=envir)

+	nuA.se[is.complete, p] <- get("nu.se", envir=envir)

+	phiA.se[is.complete, p] <- get("phi.se", envir=envir)

 	if(NOHET){

 		IB <- IB[, c(1, 3)]

@@ -912,10 +923,14 @@ coefs <- function(plateIndex, conf, MIN.OBS=3, envir, CONF.THR=0.99){

 	Ystar <- IB*W

 	is.complete <- rowSums(is.na(W)) == 0

 	nuphiAllele(allele="B", Ystar=Ystar[is.complete, ], W=W[is.complete, ], envir=envir, p=p)

-	nuB[is.complete, p] <- nu

-	phiB[is.complete, p] <- phi

-	nuB.se[is.complete, p] <- nu.se

-	phiB.se[is.complete, p] <- phi.se

+        ## ROB: can you please double check that my fix is okay?

+        ## ROB: the parameters nu/phi/nu.se/phi.se aren't defined

+        ## ROB: in this particular function. So I assume they come

+        ## ROB: from the nuphiAllele function above.

+	nuB[is.complete, p] <- get("nu", envir=envir)

+	phiB[is.complete, p] <- get("phi", envir=envir)

+	nuB.se[is.complete, p] <- get("nu.se", envir=envir)

+	phiB.se[is.complete, p] <- get("phi.se", envir=envir)

 	phiA <- matrix(as.integer(phiA), nrow(phiA), ncol(phiA))

 	phiB <- matrix(as.integer(phiB), nrow(phiA), ncol(phiA))

@@ -2,7 +2,6 @@

 ### FOR CRLMM

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

 - Decide on output format (BC vote: eSet-like)

-- Helper to convert to snpMatrix

 - Add RS ids to annotation packages

 - Allele plots

 - M v S plots

@@ -11,19 +10,6 @@

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

 ### FOR CNRMA

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

-- fix the following 2 items

-* checking R code for possible problems ... NOTE

-cnrma: no visible global function definition for ‘getCnvFid’

-cnrma: no visible binding for global variable ‘reference’

-coefs: no visible binding for global variable ‘nu’

-coefs: no visible binding for global variable ‘phi’

-coefs: no visible binding for global variable ‘nu.se’

-coefs: no visible binding for global variable ‘phi.se’

-

-* checking for unstated dependencies in R code ... WARNING

-'library' or 'require' calls not declared from:

-  affyio splines Biobase genefilter

-

-* checking for missing documentation entries ... WARNING

-Undocumented code objects:

-  computeCnBatch

+- Rob, can you run a: 'grep ROB *' under R/? There are

+  some notes for you there. Basically because I changed

+  a few things that I'm not so sure of.