@@ -410,3 +410,6 @@ Such files arise when scanner settings contain the line <GenerateVersionTwoIdatF

 If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 

 then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

  * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)

+

+2010-03-05 M. Ritchie - committed version 1.5.29

+ * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd

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

 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: 1.5.28

-Date: 2010-03-02

+Version: 1.5.29

+Date: 2010-03-05

 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>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

@@ -61,7 +61,7 @@ importFrom(mvtnorm, dmvnorm)

 importFrom(ellipse, ellipse)

 exportMethods(copyNumber)

-export(cnOptions, crlmm, crlmmIllumina, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam) 

+export(cnOptions, crlmm, crlmmIllumina, crlmmIlluminaV2, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam) 

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

@@ -68,7 +68,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE,

   intensities, not both.  Alternatively if \code{crlmmIllumina} has been

   run already with \code{save.it=TRUE}, the preprocessed data can be

   loaded from file by specifying \code{load.it=TRUE} and

-  \code{intensityFile} (\code{RG} or \code{XY} are not needed in this case).

+  \code{snpFile} (\code{RG} or \code{XY} are not needed in this case).

 }

 \references{

@@ -91,4 +91,5 @@ crlmmIllumina(RG, XY, stripNorm=TRUE,

 \examples{

 ## crlmmOut = crlmmIllumina(RG)

 }

+\seealso{\code{\link{readIdatFiles}, \code{\link{crlmmIlluminaV2}}}

 \keyword{classif}

new file mode 100644

@@ -0,0 +1,123 @@

+\name{crlmmIlluminaV2}

+\alias{crlmmIlluminaV2}

+\title{Read and Genotype Illumina Infinium II BeadChip data with CRLMM}

+\description{

+  Implementation of the CRLMM algorithm for

+  data from Illumina's Infinium II BeadChips.

+}

+\usage{

+

+crlmmIlluminaV2(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

+      arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),

+      highDensity=FALSE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"),

+      saveDate=FALSE, save.rg=FALSE, rgFile,

+      stripNorm=TRUE, useTarget=TRUE, row.names=TRUE, col.names=TRUE,

+      probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5, gender=NULL,

+      seed=1, save.ab=FALSE, snpFile, cnFile,

+      mixtureSampleSize=10^5, eps=0.1, verbose=TRUE,

+      cdfName, sns, recallMin=10, recallRegMin=1000,

+      returnParams=FALSE, badSNP=.7)

+}

+

+\arguments{

+  \item{sampleSheet}{\code{data.frame} containing Illumina sample sheet

+    information (for required columns, refer to BeadStudio Genotyping

+    guide - Appendix A).}

+  \item{arrayNames}{character vector containing names of arrays to be

+    read in.  If \code{NULL}, all arrays that can be found in the

+    specified working directory will be read in.}

+  \item{ids}{vector containing ids of probes to be read in.  If

+    \code{NULL} all probes found on the first array are read in.}

+  \item{path}{character string specifying the location of files to be

+    read by the function}

+  \item{arrayInfoColNames}{(used when \code{sampleSheet} is specified)

+    list containing elements 'barcode' which indicates column names in

+    the \code{sampleSheet} which contains the arrayNumber/barcode number

+    and 'position' which indicates the strip number.  In older style

+    sample sheets, this information is combined (usually in a column

+    named 'SentrixPosition') and this should be specified as

+    \code{list(barcode=NULL, position="SentrixPosition")}}

+  \item{highDensity}{logical (used when \code{sampleSheet} is

+    specified). If \code{TRUE}, array extensions '\_A', '\_B' in

+    sampleSheet are replaced with 'R01C01', 'R01C02' etc.}

+  \item{sep}{character string specifying separator used in .idat file

+    names.}

+  \item{fileExt}{list containing elements 'Green' and 'Red' which

+    specify the .idat file extension for the Cy3 and Cy5 channels.}

+  \item{saveDate}{'logical'.  Should the dates from each .idat be saved

+    with sample information?}

+  \item{save.rg}{'logical'. Save RG data read in from idat files?}

+  \item{rgFile}{'character' specifying filename to use to save RG data.}

+  \item{stripNorm}{'logical'.  Should the data be strip-level normalized?}

+  \item{useTarget}{'logical' (only used when \code{stripNorm=TRUE}).

+    Should the reference HapMap intensities be used in strip-level normalization?}

+  \item{row.names}{'logical'. Use rownames - SNP names?}

+  \item{col.names}{'logical'. Use colnames - Sample names?}

+  \item{probs}{'numeric' vector with priors for AA, AB and BB.}

+  \item{DF}{'integer' with number of degrees of freedom to use with t-distribution.}

+  \item{SNRMin}{'numeric' scalar defining the minimum SNR used to filter

+  out samples.}

+  \item{gender}{'integer' vector, with same length as 'filenames',

+    defining sex. (1 - male; 2 - female)}

+  \item{seed}{'integer' scalar for random number generator (used to

+    sample \code{mixtureSampleSize} SNPs for mixture model.}

+  \item{save.it}{'logical'. Save preprocessed SNP and copy number data?}

+  \item{load.it}{'logical'. Load preprocessed SNP data to speed up analysis?}

+  \item{snpFile}{'character' with filename of preprocessed SNP data to

+    be saved/loaded.}

+  \item{cnFile}{'character' with filename of preprocessed copy number 

+    data to be saved.}

+  \item{mixtureSampleSize}{'integer'. The number of SNP's to be used

+    when fitting the mixture model.}

+  \item{eps}{Minimum change for mixture model.}

+  \item{verbose}{'logical'.}

+  \item{cdfName}{'character' defining the chip annotation (manifest) to use

+    ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',

+    'human370quadv3c', 'human610quadv1b', 'human660quadv1a',

+    'human1mduov3b', 'humanomni1quadv1b')}

+  \item{sns}{'character' vector with sample names to be used.}

+  \item{recallMin}{'integer'. Minimum number of samples for recalibration.}

+  \item{recallRegMin}{'integer'. Minimum number of SNP's for regression.}

+  \item{returnParams}{'logical'. Return recalibrated parameters.}

+  \item{badSNP}{'numeric'. Threshold to flag as bad SNP (affects batchQC)}

+}

+\value{

+  A \code{SnpSet} object which contains

+  \item{calls}{Genotype calls (1 - AA, 2 - AB, 3 - BB)}

+  \item{callProbability}{confidence scores 'round(-1000*log2(1-p))'}

+  in the \code{assayData} slot and

+  \item{SNPQC}{SNP Quality Scores}

+  \item{batchQC}{Batch Quality Scores}

+  along with center and scale parameters when \code{returnParams=TRUE}

+  in the \code{featureData} slot.

+}

+

+\details{

+  This function combines the reading of data from idat files using 

+  \code{readIdatFiles} and genotyping to reduce memory.  

+}

+

+\references{

+  Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.

+  R/Bioconductor software for Illumina's Infinium whole-genome 

+  genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.

+

+  Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration,

+  normalization, and genotype calls of high-density oligonucleotide SNP

+  array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec

+  22. PMID: 17189563.

+

+  Carvalho BS, Louis TA, Irizarry RA. 

+  Quantifying uncertainty in genotype calls.

+  Bioinformatics. 2010 Jan 15;26(2):242-9.

+}

+

+\author{Matt Ritchie}

+

+\examples{

+## crlmmOut = crlmmIlluminaV2(samples,path=path,arrayInfoColNames=list(barcode="Chip",position="Section"),

+##                             saveDate=TRUE,cdfName="human370v1c",returnParams=TRUE)

+

+}

+\seealso{\code{\link{crlmmIllumina}}, \code{\link{readIdatFiles}}}

+\keyword{classif}