1. affxparser
  2. R
  3. private.assertMap.R
Browse code

o Added an Authors@R field to DESCRIPTION. o Recompiled the Rdoc-to-Rd help files using R 1.13.0, i.e. R.oo::compileRdoc().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@74592 bc3139a8-67e5-0310-9ffc-ced21a209358

H Bengtsson authored on 20/03/2013 03:34:49
Showing 1 changed files
R/private.assertMap.R
History View file @ 76cf4b2
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@@ -20,7 +20,7 @@
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 #   map, otherwise an error is thrown.
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 # }
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 #
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-# @author
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+# @author "HB"
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 #
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 # @keyword "file"
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 # @keyword "IO"
Browse code

o Added cdfAddPlasqTypes(). o Now readCdfUnits(..., readDirections=TRUE) returns group directions. o Now readCdf() reads all unit and group fields by default (as it used to). o In addition to optimizing IO time, read maps can be used to unrotate CEL data rotated by the dChip software. For more information, see help on "Cell-index maps for reading and writing". o BUG FIX: Using read maps for readCel() would give an error saying the read map is invalid even when it is not.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@21818 bc3139a8-67e5-0310-9ffc-ced21a209358

Henrik Bengtsson authored on 05/01/2007 07:26:25
Showing 1 changed files
R/private.assertMap.R
History View file @ 9d93fc4
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@@ -1,4 +1,4 @@
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-#########################################################################/**
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+#########################################################################/-Rdoc TURNED OFF-**
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 # @RdocFunction .assertMap
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 #
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 # @title "Validates a read or a write map"
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 # @keyword "file"
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 # @keyword "IO"
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 # @keyword "internal"
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-#*/#########################################################################
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+#*-Rdoc TURNED OFF-/#########################################################################
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 .assertMap <- function(map, nbrOfCells=length(map), ...) {
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   n <- length(map);
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   if (n != nbrOfCells) {
Browse code

o Added convertCel() and compareCels(). These need to be documented. o Added argument 'writeMap' to updateCel(). o BUG FIX: Using argument 'readMap' in readCel() would give an error.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affxparser@21794 bc3139a8-67e5-0310-9ffc-ced21a209358

Henrik Bengtsson authored on 04/01/2007 07:55:41
Showing 1 changed files
R/private.assertMap.R
History View file @ 63b4c96
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new file mode 100644
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+#########################################################################/**
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+# @RdocFunction .assertMap
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+#
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+# @title "Validates a read or a write map"
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+#
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+# @synopsis
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+#
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+# \description{
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+#   @get "title".
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+# }
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+#
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+# \arguments{
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+#   \item{map}{An @integer @vector.}
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+#   \item{nbrOfCells}{The number of cells on the array.}
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+#   \item{...}{Not used.}
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+# }
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+#
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+# \value{
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+#   Returns (invisibly) the map as an @integer @vector, if it is a valid
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+#   map, otherwise an error is thrown.
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+# }
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+#
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+# @author
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+#
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+# @keyword "file"
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+# @keyword "IO"
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+# @keyword "internal"
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+#*/#########################################################################
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+.assertMap <- function(map, nbrOfCells=length(map), ...) {
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+  n <- length(map);
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+  if (n != nbrOfCells) {
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+    stop("Argument 'map' is not a valid map. The number of elements does not match the number of cells on the array: ", n, " != ", nbrOfCells);
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+  }
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+
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+  # Coerce to integers
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+  map <- as.integer(map);
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+
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+  # Assert that there are no NAs
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+  r <- range(map);
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+  if (any(is.na(r))) {
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+    stop("Argument 'map' is not a valid map. It contains NA values.");
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+  }
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+
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+  # Check range
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+  if (r[1] != 1 || r[2] != nbrOfCells) {
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+    stop("Argument 'map' is not a valid map. Its range is not [1,",
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+                            nbrOfCells, "]: ", "[", r[1], ", ", r[2], "]");
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+  }
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+
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+  # Check that the map is bijective
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+#  map2 <- invertMap(invertMap(map));
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+#  if (!identical(map, map2)) {
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+#    stop("Argument 'map' is not a valid map. It is not bijective.");
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+#  }
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+
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+  invisible(map);
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+} # .assertMap()
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+
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+
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+############################################################################
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+# HISTORY:
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+# 2007-01-04
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+# o Created.
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+############################################################################