@@ -1,13 +1,13 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling via CRLMM Algorithm

-Version: 1.27

+Version: 1.0.29

 Date: 2008-12-28

 Author: Rafael A Irizarry

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays.

-License: Artistic-2.0

 Depends: methods, affyio, preprocessCore, utils

+License: Artistic-2.0

 Suggests: hapmapsnp5, genomewidesnp5Crlmm

 Collate: crlmmGT.R

          crlmm.R

@@ -1,4 +1,8 @@

 useDynLib("crlmm")

-import(methods)

+import(methods, utils)

 export("crlmm",

        "list.celfiles")

+

+importFrom(affyio, read.celfile.header, read.celfile)

+

+importFrom(preprocessCore, normalize.quantiles.use.target)

@@ -1,4 +1,5 @@

 snprma <- function(filenames, mixtureSampleSize=10^5, fitMixture=FALSE, eps=0.1, verbose=TRUE, seed=1, cdfName, sns){

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

   ##ADD CHECK TO SEE IF LOADED

   if (missing(cdfName))

     cdfName <- read.celfile.header(filenames[1])$cdfName

Binary files a/inst/doc/crlmm.pdf and b/inst/doc/crlmm.pdf differ

@@ -58,6 +58,18 @@ recallRegMin = 1000, returnParams = FALSE, badSNP = 0.7)

   Carvalho B, Louis TA, Irizarry RA. Describing Uncertainty in

   Genome-wide Genotype Calling. (in prep)

 }

+\examples{

+## this can be slow

+if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){

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

+  crlmmOutput[["calls"]][1:10, 1:2]

+  crlmmOutput[["confs"]][1:10, 1:2]

+}

+}

 \keyword{classif}

@@ -25,5 +25,21 @@ list.celfiles(...)

   methods. In this situations, it is safer to use the argument 'full.names=TRUE'.

 }

 \seealso{\code{\link{list.files}}}

+\examples{

+if (require(hapmapsnp5)){

+  path <- system.file("celFiles", package="hapmapsnp5")

+

+  ## only the filenames

+  list.celfiles(path)

+

+  ## the filenames with full path...

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

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

+}else{

+  ## this won't return anything

+  ## if in the working directory there isn't any CEL

+  list.celfiles(getwd())

+}

+}

 \keyword{IO}

 \keyword{utilities}