Add values alias to elementMetadata accessor and setter.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@45527 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Mar 26, 2010 · 8e72d66 · 8e72d66
1 parent 47666e1
commit 8e72d66
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Showing 4 changed files with 17 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,7 @@ Version: 0.0.10
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Biocore Team c/o BioC user list <[email protected]>
 biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation
-Depends: R (>= 2.8.0), methods, IRanges (>= 1.5.67)
+Depends: R (>= 2.8.0), methods, IRanges (>= 1.5.71)
 Imports: methods, IRanges
 LinkingTo: IRanges
 Suggests: RUnit, GenomicFeatures, BSgenome

diff --git a/R/GRanges-class.R b/R/GRanges-class.R
@@ -737,8 +737,8 @@ setMethod("show", "GRanges",
         nc <- ncol(object@elementMetadata)
         cat(class(object), " with ",
             lo, ifelse(lo == 1, " range and ", " ranges and "),
-            nc, ifelse(nc == 1, " elementMetadata column\n",
-                       " elementMetadata columns\n"),
+            nc, ifelse(nc == 1, " elementMetadata value\n",
+                       " elementMetadata values\n"),
             sep = "")
         if (lo == 0) {
             out <-

diff --git a/man/GRanges-class.Rd b/man/GRanges-class.Rd
@@ -155,6 +155,10 @@
       Gets or sets the optional data columns. \code{value} can be a DataFrame,
       data.frame object, or NULL.
     }
+    \item{}{
+      \code{values(x), values(x) <- value}:
+      Alternative to \code{elementMetadata} functions.
+    }
     \item{}{
       \code{names(x)}, \code{names(x) <- value}:
       Gets or sets the names of the elements.
@@ -397,7 +401,7 @@
   # Summarizing elements
   table(seqnames(gr))
   sum(width(gr))
-  summary(elementMetadata(gr)[,"score"])
+  summary(elementMetadata(gr)[,"score"]) # or values(gr)
   coverage(gr)
 
   # Changing sequence name

diff --git a/man/GRangesList-class.Rd b/man/GRangesList-class.Rd
@@ -107,6 +107,15 @@
       Gets or sets the seqlengths. \code{value} can be a named non-negative
       integer or numeric vector.
     }
+    \item{}{
+      \code{elementMetadata(x)}, \code{elementMetadata(x) <- value}:
+      Gets or sets the optional data columns for the GRangesList elements.
+      \code{value} can be a DataFrame, data.frame object, or NULL.
+    }
+    \item{}{
+      \code{values(x), values(x) <- value}:
+      Alternative to \code{elementMetadata} functions.
+    }
   }
 }