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

 Package: affxparser

-Version: 1.17.2

-Date: 2009-05-10

+Version: 1.17.3

+Date: 2009-05-29

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan

 Maintainer: Kasper Daniel Hansen <[email protected]>

new file mode 100644

@@ -0,0 +1,44 @@

+########################################################################/**

+# @RdocFunction applyCdfGroupFields

+#

+# @title "Applies a function to a list of fields of each group in a CDF structure"

+#

+# \description{

+#  @get "title".

+# }

+#

+# @synopsis

+#

+# \arguments{

+#  \item{cdf}{A CDF @list structure.}

+#  \item{fcn}{A @function that takes a @list structure of fields

+#             and returns an updated @list of fields.}

+#  \item{...}{Arguments passed to the \code{fcn} function.}

+# }

+#

+# \value{

+#  Returns an updated CDF @list structure.

+# }

+#

+# @author

+#

+# \seealso{

+#   @see "applyCdfGroups".

+# }

+#

+# @keyword programming

+#**/####################################################################### 

+applyCdfGroupFields <- function(cdf, fcn, ...) {

+  applyCdfGroups(cdf, function(groups) {

+    lapply(groups, FUN=fcn, ...);

+  });

+} # applyCdfGroupFields()

+

+

+

+############################################################################

+# HISTORY:

+# 2009-05-29

+# o Added Rdoc comments.

+# o Created.

+############################################################################

@@ -6,8 +6,7 @@

 # \description{

 #  @get "title".

 #

-#  This @function is design to be used with @see "applyCdfGroups"

-#  on an Affymetrix Mapping (SNP) CDF @list structure.

+#  This @function is designed to be used with @see "applyCdfGroups".

 # }

 #

 # @synopsis

@@ -6,8 +6,7 @@

 # \description{

 #  @get "title".

 #

-#  This @function is design to be used with @see "applyCdfGroups"

-#  on an Affymetrix Mapping (SNP) CDF @list structure.

+#  This @function is designed to be used with @see "applyCdfGroups".

 # }

 #

 # @synopsis

new file mode 100644

@@ -0,0 +1,60 @@

+########################################################################/**

+# @RdocFunction cdfSetDimension

+#

+# @title "Sets the dimension of an object"

+#

+# \description{

+#  @get "title".

+#

+#  This @function is designed to be used with @see "applyCdfGroupFields".

+# }

+#

+# @synopsis

+#

+# \arguments{

+#  \item{groups}{A @list of groups.}

+#  \item{which}{An @integer or @character @vector of groups be returned.}

+#  \item{...}{Not used.}

+# }

+#

+# \value{

+#  Returns a @list structure of groups.

+# }

+#

+# \seealso{

+#  @see "applyCdfGroupFields".

+# }

+#

+# @author

+#

+# @keyword programming

+# @keyword internal

+#**/####################################################################### 

+cdfSetDimension <- function(field, dim, ...) {

+  n <- length(field);

+  ndim <- length(dim);

+

+  naDim <- whichVector(is.na(dim));

+  if (length(naDim) > 0) {

+    if (length(naDim) > 1) {

+      stop("Cannot infer dimension. Only one of the dimension can be unknown: ", paste(dim, collapse="x"));

+    }

+    dimNA <- n / prod(dim[-naDim]);

+    if (dimNA %% 1 == 0) {

+      dim[naDim] <- dimNA;

+      dim(field) <- dim;

+    }

+  } else if (n == prod(dim)) {

+    dim(field) <- dim;

+  }

+

+  field;

+} # cdfSetDimension()

+

+

+############################################################################

+# HISTORY:

+# 2009-05-29

+# o Added Rdoc comments.

+# o Created.

+############################################################################

@@ -1,6 +1,28 @@

 Package: affxparser

 ===================

+Version: 1.17.3 [2009-05-29]

+o Added applyCdfGroupFields() and cdfSetDimension().

+

+

+Version: 1.17.2 [2009-02-20]

+o BUG FIX: readChp() would crash (segmentation fault) for (at least)

+  some CHP files for GenomeWideSNP_5 generated by Affymetrix Power Tools.

+o BUG FIX: Updated compareCels() to work with new readCelHeader().

+

+

+Version: 1.17.1 [2009-05-09]

+o Now readCelHeader() also reads DAT headers from Calvin CEL files.

+

+

+Version: 1.17.0 [2009-04-20]

+o Devel version bumped because of the new Bioconductor release.

+

+

+Version: 1.16.0 [2009-04-20]

+o Release version bumped because of the new Bioconductor release.

+

+

 Version: 1.15.6 [2009-02-20]

 o Added optional argument 'newChipType' to convertCel() for overriding

   the default chip type.  Useful for updating the formal chip type 

@@ -15,8 +15,7 @@

 \description{

  Gets a subset of groups fields in a CDF structure.

- This \code{\link[base]{function}} is design to be used with \code{\link{applyCdfGroups}}()

- on an Affymetrix Mapping (SNP) CDF \code{\link[base]{list}} structure.

+ This \code{\link[base]{function}} is designed to be used with \code{\link{applyCdfGroups}}().

 }

 \usage{cdfGetFields(groups, fields, ...)}

@@ -15,8 +15,7 @@

 \description{

  Gets a subset of groups in a CDF structure.

- This \code{\link[base]{function}} is design to be used with \code{\link{applyCdfGroups}}()

- on an Affymetrix Mapping (SNP) CDF \code{\link[base]{list}} structure.

+ This \code{\link[base]{function}} is designed to be used with \code{\link{applyCdfGroups}}().

 }

 \usage{cdfGetGroups(groups, which, ...)}

@@ -6,39 +6,39 @@

 % by the Rdoc compiler part of the R.oo package.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

- \name{compareCels}

+\name{compareCels}

 \alias{compareCels}

- \title{Compares the contents of two CEL files}

+\title{Compares the contents of two CEL files}

- \usage{compareCels(pathname, other, readMap=NULL, otherReadMap=NULL, verbose=0, ...)}

+\usage{compareCels(pathname, other, readMap=NULL, otherReadMap=NULL, verbose=0, ...)}

- \description{

-   Compares the contents of two CEL files.

- }

+\description{

+  Compares the contents of two CEL files.

+}

- \arguments{

-   \item{pathname}{The pathname of the first CEL file.}

-   \item{other}{The pathname of the seconds CEL file.}

-   \item{readMap}{An optional read map for the first CEL file.}

-   \item{otherReadMap}{An optional read map for the second CEL file.}

-   \item{verbose}{An \code{\link[base]{integer}}. The larger the more details are printed.}

-   \item{...}{Not used.}

- }

+\arguments{

+  \item{pathname}{The pathname of the first CEL file.}

+  \item{other}{The pathname of the seconds CEL file.}

+  \item{readMap}{An optional read map for the first CEL file.}

+  \item{otherReadMap}{An optional read map for the second CEL file.}

+  \item{verbose}{An \code{\link[base]{integer}}. The larger the more details are printed.}

+  \item{...}{Not used.}

+}

- \value{

-   Returns \code{\link[base:logical]{TRUE}} if the two CELs are equal, otherwise \code{\link[base:logical]{FALSE}}.  If \code{\link[base:logical]{FALSE}},

-   the attribute \code{reason} contains a string explaining what

-   difference was detected, and the attributes \code{value1} and

-   \code{value2} contain the two objects/values that differs.

- }

+\value{

+  Returns \code{\link[base:logical]{TRUE}} if the two CELs are equal, otherwise \code{\link[base:logical]{FALSE}}.  If \code{\link[base:logical]{FALSE}},

+  the attribute \code{reason} contains a string explaining what

+  difference was detected, and the attributes \code{value1} and

+  \code{value2} contain the two objects/values that differs.

+}

- \author{Henrik Bengtsson (\url{http://www.braju.com/R/})}

+\author{Henrik Bengtsson (\url{http://www.braju.com/R/})}

- \seealso{

-   \code{\link{convertCel}}().

- }

+\seealso{

+  \code{\link{convertCel}}().

+}

@@ -12,7 +12,7 @@

  \title{Converts a CEL into the same CEL but with another format}

- \usage{convertCel(filename, outFilename, readMap=NULL, writeMap=NULL, version="4", newChipType = NULL, ..., .validate=FALSE, verbose=FALSE)}

+ \usage{convertCel(filename, outFilename, readMap=NULL, writeMap=NULL, version="4", newChipType=NULL, ..., .validate=FALSE, verbose=FALSE)}

  \description{

    Converts a CEL into the same CEL but with another format.

@@ -28,7 +28,7 @@

    \item{writeMap}{An optional write map for the output CEL file.}

    \item{version}{The version of the output file format.}

    \item{newChipType}{An optional string for overriding the chip type

-     in the CEL file header.}

+      in the CEL file header.}

    \item{...}{Not used.}

    \item{.validate}{If \code{\link[base:logical]{TRUE}}, a consistency test between the generated

      and the original CEL is performed.}