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

 Package: Biobase

 Title: Biobase: Base functions for Bioconductor

-Version: 2.31.2

+Version: 2.31.3

 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon

 Description: Functions that are needed by many other packages or which

         replace R functions.

@@ -8,7 +8,7 @@ importFrom(BiocGenerics,

     annotation, "annotation<-"

 )

-importFrom(utils, head)

+importFrom(utils, head, tail)

 exportClasses(aggregator, container, eSet,

               MIAxE, MIAME, characterORMIAME,

@@ -62,3 +62,4 @@ export(.DollarNames.eSet,

        lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery,

        validMsg, write.AnnotatedDataFrame)

 S3method(head, "AnnotatedDataFrame")

+S3method(tail, "AnnotatedDataFrame")

@@ -4,7 +4,7 @@ CHANGES IN VERSION 2.31

 NEW FEATURES

     o tab completion implemented for eSet classes

-    o head.AnnotatedDataFrame method introduced

+    o head and tail.AnnotatedDataFrame methods introduced

 CHANGES IN VERSION 2.27

 -----------------------

@@ -115,9 +115,8 @@ setMethod("annotatedDataFrameFrom",

           signature(object="AssayData"),

           annotatedDataFrameFromAssayData)

-head.AnnotatedDataFrame <-

-    function(x, n=6L, ...)

-{

+head.AnnotatedDataFrame <- function(x, n=6L, ...) {

+    ## essentially, utils:::head.data.frame

     stopifnot(length(x) == 1L)

     n <- if (n < 0L) {

         max(nrow(x) + n, 0L)

@@ -125,6 +124,16 @@ head.AnnotatedDataFrame <-

     x[seq_len(n), ]

 }

+tail.AnnotatedDataFrame <- function(x, n=6L, ...) {

+    ## essentially, utils:::tail.data.frame

+    stopifnot(length(x) == 1L)

+    nrx <- nrow(x)

+    n <- if (n < 0L) 

+        max(nrx + n, 0L)

+    else min(n, nrx)

+    x[seq.int(to = nrx, length.out = n), , drop = FALSE]

+}

+

 setMethod("dimnames", "AnnotatedDataFrame", function(x) {

     dimnames(pData(x))

 })

@@ -21,6 +21,7 @@

 \alias{coerce,data.frame,AnnotatedDataFrame-method}

 \alias{coerce,phenoData,AnnotatedDataFrame-method}

 \alias{head.AnnotatedDataFrame}

+\alias{tail.AnnotatedDataFrame}

 \alias{dim,AnnotatedDataFrame-method}

 \alias{dimnames,AnnotatedDataFrame-method}

 \alias{dimnames<-,AnnotatedDataFrame-method}

@@ -162,9 +163,10 @@ an \code{AnnotatedDataFrame} from \code{\link{AssayData-class}}.

       \code{$<variable> <- <new_value>}:}{Replace or add a variable to

       \code{pData}. ... can include named arguments (especially

       \code{labelDescription}) to be added to \code{varMetadata}.}

-    \item{\code{head(<AnnotatedDataFrame>), n = 6L}}{Subset up to

-      \code{n} rows; negative \code{n} returns the first \code{nrow() -

-      n} rows.}

+    \item{\code{head(<AnnotatedDataFrame>, n = 6L, ...)},

+      \code{tail(<AnnotatedDataFrame>, n=6L, ...)}}{Select the first

+      (last for tail) \code{n} rows; negative \code{n} returns the first

+      (last) \code{nrow() - n} rows.}

     \item{\code{dim(<AnnotatedDataFrame>)},

       \code{ncol(<AnnotatedDataFrame>)}:}{Number of samples and

       variables (\code{dim}) and variables (\code{ncol}) in the