@@ -14,7 +14,7 @@ readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",

                                      position="SentrixPosition_A"),

               highDensity=FALSE, sep="_",

               fileExt=list(green="Grn.idat", red="Red.idat"),

-              saveDate=FALSE)

+              saveDate=FALSE, verbose=FALSE)

 }

 \arguments{

@@ -44,6 +44,7 @@ readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",

     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{verbose}{logical.  Should processing information be displayed as data is read in?}

 }

 \details{

@@ -1,5 +1,6 @@

 \name{readIdatFiles}

 \alias{readIdatFiles}

+\alias{readIdatFiles2}

 \title{Reads Idat Files from Infinium II Illumina BeadChips}

@@ -62,6 +62,12 @@ Thanks to Keith Baggerly who provided the code to read in the binary .idat files

   for SNPs with 0 beads (\code{zero}) for each bead type.

 }

+\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.

+}

+

 \author{Matt Ritchie}

 \examples{

@@ -46,8 +46,7 @@ readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",

 }

 \details{

-The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that

-were used in each channel and standard errors (all on the orginal scale)

+The summarised Cy3 (G) and Cy5 (R) intensities (on the orginal scale)

 are read in from the .idat files.

 Where available, a \code{sampleSheet} data.frame, in the same format

@@ -59,9 +58,8 @@ Thanks to Keith Baggerly who provided the code to read in the binary .idat files

 }

 \value{

-  NChannelSet with intensity data (\code{R}, \code{G}), number of beads

-  (\code{Rnb}, \code{Gnb}) and standard errors (\code{Rse}, \code{Gse})

-  for each bead type.

+  NChannelSet with intensity data (\code{R}, \code{G}), and indicator 

+  for SNPs with 0 beads (\code{zero}) for each bead type.

 }

 \author{Matt Ritchie}

new file mode 100644

@@ -0,0 +1,74 @@

+\name{readIdatFiles}

+\alias{readIdatFiles}

+

+\title{Reads Idat Files from Infinium II Illumina BeadChips}

+

+\description{

+  Reads intensity information for each bead type from

+  .idat files of Infinium II genotyping BeadChips}

+

+\usage{

+readIdatFiles(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)

+}

+

+\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?}

+}

+

+\details{

+The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that

+were used in each channel and standard errors (all on the orginal scale)

+are read in from the .idat files.

+

+Where available, a \code{sampleSheet} data.frame, in the same format

+as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and

+'SentrixPosition\_A' are required) which keeps track of sample

+information can be specified.

+

+Thanks to Keith Baggerly who provided the code to read in the binary .idat files.

+}

+

+\value{

+  NChannelSet with intensity data (\code{R}, \code{G}), number of beads

+  (\code{Rnb}, \code{Gnb}) and standard errors (\code{Rse}, \code{Gse})

+  for each bead type.

+}

+

+\author{Matt Ritchie}

+

+\examples{

+

+#RG = readIdatFiles()

+

+}

+\keyword{IO}

deleted file mode 100644

@@ -1,74 +0,0 @@

-\name{readIdatFiles}

-\alias{readIdatFiles}

-

-\title{Reads Idat Files from Infinium II Illumina BeadChips}

-

-\description{

-  Reads intensity information for each bead type from

-  .idat files of Infinium II genotyping BeadChips}

-

-\usage{

-readIdatFiles(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)

-}

-

-\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?}

-}

-

-\details{

-The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that

-were used in each channel and standard errors (all on the orginal scale)

-are read in from the .idat files.

-

-Where available, a \code{sampleSheet} data.frame, in the same format

-as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and

-'SentrixPosition\_A' are required) which keeps track of sample

-information can be specified.

-

-Thanks to Keith Baggerly who provided the code to read in the binary .idat files.

-}

-

-\value{

-  NChannelSet with intensity data (\code{R}, \code{G}), number of beads

-  (\code{Rnb}, \code{Gnb}) and standard errors (\code{Rse}, \code{Gse})

-  for each bead type.

-}

-

-\author{Matt Ritchie}

-

-\examples{

-

-#RG = readIdatFiles()

-

-}

-\keyword{IO}

@@ -8,7 +8,7 @@

   .idat files of Infinium II genotyping BeadChips}

 \usage{

-readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

+readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",

               arrayInfoColNames=list(barcode="SentrixBarcode_A",

                                      position="SentrixPosition_A"),

               highDensity=FALSE, sep="_",

@@ -35,7 +35,7 @@ readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

     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

+    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.}

@@ -51,8 +51,8 @@ were used in each channel and standard errors (all on the orginal scale)

 are read in from the .idat files.

 Where available, a \code{sampleSheet} data.frame, in the same format

-as used by BeadStudio (columns 'Sample_ID', 'SentrixBarcode_A' and

-'SentrixPosition_A' are required) which keeps track of sample

+as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and

+'SentrixPosition\_A' are required) which keeps track of sample

 information can be specified.

 Thanks to Keith Baggerly who provided the code to read in the binary .idat files.

old mode 100755

new mode 100644

@@ -12,7 +12,8 @@ readIdatFiles(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"))

+              fileExt=list(green="Grn.idat", red="Red.idat"),

+              saveDate=FALSE)

 }

 \arguments{

@@ -40,6 +41,8 @@ readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",

     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?}

 }

 \details{

new file mode 100755

@@ -0,0 +1,71 @@

+\name{readIdatFiles}

+\alias{readIdatFiles}

+

+\title{Reads Idat Files from Infinium II Illumina BeadChips}

+

+\description{

+  Reads intensity information for each bead type from

+  .idat files of Infinium II genotyping BeadChips}

+

+\usage{

+readIdatFiles(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"))

+}

+

+\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.}

+}

+

+\details{

+The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that

+were used in each channel and standard errors (all on the orginal scale)

+are read in from the .idat files.

+

+Where available, a \code{sampleSheet} data.frame, in the same format

+as used by BeadStudio (columns 'Sample_ID', 'SentrixBarcode_A' and

+'SentrixPosition_A' are required) which keeps track of sample

+information can be specified.

+

+Thanks to Keith Baggerly who provided the code to read in the binary .idat files.

+}

+

+\value{

+  NChannelSet with intensity data (\code{R}, \code{G}), number of beads

+  (\code{Rnb}, \code{Gnb}) and standard errors (\code{Rse}, \code{Gse})

+  for each bead type.

+}

+

+\author{Matt Ritchie}

+

+\examples{

+

+#RG = readIdatFiles()

+

+}

+\keyword{IO}