[med-svn] [r-bioc-biobase] 03/07: Imported Upstream version 2.32.0
Andreas Tille
tille at debian.org
Tue Oct 25 19:51:30 UTC 2016
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tille pushed a commit to branch master
in repository r-bioc-biobase.
commit 48203a6e511e62d7357708ed47b7d1292e0279dd
Author: Andreas Tille <tille at debian.org>
Date: Sun May 8 08:11:01 2016 +0200
Imported Upstream version 2.32.0
---
DESCRIPTION | 4 ++--
NAMESPACE | 7 ++++++-
NEWS | 8 ++++++++
R/methods-AnnotatedDataFrame.R | 19 +++++++++++++++++++
R/methods-eSet.R | 3 +++
build/vignette.rds | Bin 344 -> 342 bytes
inst/doc/BiobaseDevelopment.pdf | Bin 223305 -> 246470 bytes
inst/doc/ExpressionSetIntroduction.pdf | Bin 157770 -> 174947 bytes
inst/doc/esApply.pdf | Bin 86615 -> 93110 bytes
man/class.AnnotatedDataFrame.Rd | 6 ++++++
10 files changed, 44 insertions(+), 3 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 35cff60..db8ae2a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: Biobase
Title: Biobase: Base functions for Bioconductor
-Version: 2.30.0
+Version: 2.32.0
Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
Description: Functions that are needed by many other packages or which
replace R functions.
@@ -22,4 +22,4 @@ Collate: tools.R strings.R environment.R vignettes.R packages.R
LazyLoad: yes
biocViews: Infrastructure
NeedsCompilation: yes
-Packaged: 2015-10-14 00:32:21 UTC; biocbuild
+Packaged: 2016-05-04 02:37:20 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index bcdf777..24b739e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,6 +8,8 @@ importFrom(BiocGenerics,
annotation, "annotation<-"
)
+importFrom(utils, head, tail)
+
exportClasses(aggregator, container, eSet,
MIAxE, MIAME, characterORMIAME,
annotatedDataset, AssayData, data.frameOrNULL,
@@ -46,7 +48,8 @@ exportMethods("[", "[[", "$", abstract, aggenv, aggfun,
AnnotatedDataFrame,
ExpressionSet)
-export(Aggregate, addVigs2WinMenu, anyMissing,
+export(.DollarNames.eSet,
+ Aggregate, addVigs2WinMenu, anyMissing,
as.data.frame.ExpressionSet, assayDataNew,
assayDataValidMembers, assayDataElementNames, assayDataElement,
assayDataElementReplace, "assayDataElement<-", cache, copyEnv,
@@ -58,3 +61,5 @@ export(Aggregate, addVigs2WinMenu, anyMissing,
selectSome, strbreak, subListExtract, testBioCConnection,
lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery,
validMsg, write.AnnotatedDataFrame)
+S3method(head, "AnnotatedDataFrame")
+S3method(tail, "AnnotatedDataFrame")
diff --git a/NEWS b/NEWS
index 14e91fb..439f1e5 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 2.31
+-----------------------
+
+NEW FEATURES
+
+ o tab completion implemented for eSet classes
+ o head and tail.AnnotatedDataFrame methods introduced
+
CHANGES IN VERSION 2.27
-----------------------
diff --git a/R/methods-AnnotatedDataFrame.R b/R/methods-AnnotatedDataFrame.R
index 368f885..9c7b75b 100644
--- a/R/methods-AnnotatedDataFrame.R
+++ b/R/methods-AnnotatedDataFrame.R
@@ -115,6 +115,25 @@ setMethod("annotatedDataFrameFrom",
signature(object="AssayData"),
annotatedDataFrameFromAssayData)
+head.AnnotatedDataFrame <- function(x, n=6L, ...) {
+ ## essentially, utils:::head.data.frame
+ stopifnot(length(x) == 1L)
+ n <- if (n < 0L) {
+ max(nrow(x) + n, 0L)
+ } else min(n, nrow(x))
+ x[seq_len(n), ]
+}
+
+tail.AnnotatedDataFrame <- function(x, n=6L, ...) {
+ ## essentially, utils:::tail.data.frame
+ stopifnot(length(x) == 1L)
+ nrx <- nrow(x)
+ n <- if (n < 0L)
+ max(nrx + n, 0L)
+ else min(n, nrx)
+ x[seq.int(to = nrx, length.out = n), , drop = FALSE]
+}
+
setMethod("dimnames", "AnnotatedDataFrame", function(x) {
dimnames(pData(x))
})
diff --git a/R/methods-eSet.R b/R/methods-eSet.R
index 20a2b9c..1e580ae 100644
--- a/R/methods-eSet.R
+++ b/R/methods-eSet.R
@@ -407,6 +407,9 @@ setMethod("$", "eSet", function(x, name) {
eval(substitute(phenoData(x)$NAME_ARG, list(NAME_ARG=name)))
})
+.DollarNames.eSet <- function(x, pattern)
+ grep(pattern, names(pData(x)), value=TRUE)
+
setReplaceMethod("$", "eSet", function(x, name, value) {
phenoData(x)[[name]] = value
x
diff --git a/build/vignette.rds b/build/vignette.rds
index 0ab9656..f7632d6 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/BiobaseDevelopment.pdf b/inst/doc/BiobaseDevelopment.pdf
index d2054f3..7bd21db 100644
Binary files a/inst/doc/BiobaseDevelopment.pdf and b/inst/doc/BiobaseDevelopment.pdf differ
diff --git a/inst/doc/ExpressionSetIntroduction.pdf b/inst/doc/ExpressionSetIntroduction.pdf
index c267e2a..ff875c6 100644
Binary files a/inst/doc/ExpressionSetIntroduction.pdf and b/inst/doc/ExpressionSetIntroduction.pdf differ
diff --git a/inst/doc/esApply.pdf b/inst/doc/esApply.pdf
index 96909f0..4c79bb9 100644
Binary files a/inst/doc/esApply.pdf and b/inst/doc/esApply.pdf differ
diff --git a/man/class.AnnotatedDataFrame.Rd b/man/class.AnnotatedDataFrame.Rd
index 5b9c7a7..d0356de 100644
--- a/man/class.AnnotatedDataFrame.Rd
+++ b/man/class.AnnotatedDataFrame.Rd
@@ -20,6 +20,8 @@
\alias{initialize,AnnotatedDataFrame-method}
\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}
@@ -161,6 +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, ...)},
+ \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
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