[med-svn] [r-bioc-summarizedexperiment] 01/04: New upstream version 1.8.0
Andreas Tille
tille at debian.org
Wed Nov 8 14:05:07 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-summarizedexperiment.
commit e8c5fc7bb9821553720e9210c921f3fe13edb53e
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 8 14:48:07 2017 +0100
New upstream version 1.8.0
---
DESCRIPTION | 14 +--
NAMESPACE | 2 +-
NEWS | 23 +++-
R/RangedSummarizedExperiment-class.R | 9 +-
R/findOverlaps-methods.R | 6 +-
R/makeSummarizedExperimentFromExpressionSet.R | 5 +
build/vignette.rds | Bin 210 -> 210 bytes
inst/doc/SummarizedExperiment.R | 38 +++----
inst/doc/SummarizedExperiment.html | 131 ++++++++++++++++++++---
man/findOverlaps-methods.Rd | 4 +-
man/makeSummarizedExperimentFromExpressionSet.Rd | 8 +-
11 files changed, 182 insertions(+), 58 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index eb40214..a6798b6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -4,20 +4,20 @@ Description: The SummarizedExperiment container contains one or more assays,
each represented by a matrix-like object of numeric or other mode.
The rows typically represent genomic ranges of interest and the columns
represent samples.
-Version: 1.6.5
+Version: 1.8.0
Encoding: UTF-8
Author: Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
GenomeAnnotation
-Depends: R (>= 3.2), methods, GenomicRanges (>= 1.27.22), Biobase,
- DelayedArray (>= 0.1.9)
+Depends: R (>= 3.2), methods, GenomicRanges (>= 1.29.14), Biobase,
+ DelayedArray (>= 0.3.20)
Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
- S4Vectors (>= 0.13.13), IRanges (>= 2.7.2), GenomeInfoDb (>=
- 1.11.4)
+ S4Vectors (>= 0.13.13), IRanges (>= 2.11.17), GenomeInfoDb (>=
+ 1.13.1)
Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
- digest, jsonlite, rhdf5, HDF5Array (>= 1.4.8), airway, RUnit
+ digest, jsonlite, rhdf5, HDF5Array (>= 1.5.8), airway, RUnit
VignetteBuilder: knitr
License: Artistic-2.0
Collate: Assays-class.R SummarizedExperiment-class.R
@@ -27,4 +27,4 @@ Collate: Assays-class.R SummarizedExperiment-class.R
makeSummarizedExperimentFromDataFrame.R readKallisto.R
saveHDF5SummarizedExperiment.R zzz.R
NeedsCompilation: no
-Packaged: 2017-09-29 00:11:42 UTC; biocbuild
+Packaged: 2017-10-31 00:24:34 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index eaee9f8..bda868d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -62,13 +62,13 @@ exportMethods(
coverage,
findOverlaps,
precede, follow, nearest, distance, distanceToNearest,
- acbind, arbind,
## Generics defined in GenomeInfoDb:
seqinfo, "seqinfo<-",
seqnames, "seqnames<-",
## Generics defined in DelayedArray:
+ acbind, arbind,
rowRanges, realize
)
diff --git a/NEWS b/NEWS
index cc48bc3..a202fae 100644
--- a/NEWS
+++ b/NEWS
@@ -1,11 +1,32 @@
-CHANGES IN VERSION 1.6.1
+CHANGES IN VERSION 1.8.0
------------------------
+NEW FEATURES
+
+ o Add 'chunk_dim' and 'level' arguments to saveHDF5SummarizedExperiment().
+
+ o Add coercion from ExpressionSet to SummarizedExperiment.
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+DEPRECATED AND DEFUNCT
+
+ o Remove 'force' argument from seqinfo() and seqlevels() setters (the
+ argument got deprecated in BioC 3.5 in favor of new and more flexible
+ 'pruning.mode' argument).
+
BUG FIXES
+ o Coercion from SummarizedExperiment to RangedSummarizedExperiment was
+ losing the metadata columns. Fixed now.
+
+ o Fix cbind() and rbind() of SummarizedExperiment objects when some of the
+ assays are DataFrame or data.frame objects.
+
o '$' completion on SummarizedExperiment works in RStudio and on
RangedSummarizedExperiment.
+
CHANGES IN VERSION 1.6.0
------------------------
diff --git a/R/RangedSummarizedExperiment-class.R b/R/RangedSummarizedExperiment-class.R
index e8d9dc7..6af6164 100644
--- a/R/RangedSummarizedExperiment-class.R
+++ b/R/RangedSummarizedExperiment-class.R
@@ -10,7 +10,7 @@
setClass("RangedSummarizedExperiment",
contains="SummarizedExperiment",
representation(
- rowRanges="GenomicRangesORGRangesList"
+ rowRanges="GenomicRanges_OR_GRangesList"
),
prototype(
rowRanges=GRanges()
@@ -111,7 +111,7 @@ setMethod("SummarizedExperiment", "SimpleList",
} else {
if (!missing(rowRanges))
stop("only one of 'rowData' and 'rowRanges' can be specified")
- if (is(rowData, "GenomicRangesORGRangesList")) {
+ if (is(rowData, "GenomicRanges_OR_GRangesList")) {
rowRanges <- rowData
if (is.null(names(rowRanges)))
names(rowRanges) <- .get_rownames_from_assays(assays)
@@ -145,7 +145,7 @@ setMethod("SummarizedExperiment", "SimpleList",
assays <- Assays(assays)
- if (missing(rowRanges) && !is(rowData, "GenomicRangesORGRangesList")) {
+ if (missing(rowRanges) && !is(rowData, "GenomicRanges_OR_GRangesList")) {
new_SummarizedExperiment(assays, ans_rownames, rowData, colData,
metadata)
} else {
@@ -481,7 +481,7 @@ setMethod("seqinfo", "RangedSummarizedExperiment",
})
setReplaceMethod("seqinfo", "RangedSummarizedExperiment",
- function (x, new2old= NULL, force=FALSE,
+ function (x, new2old= NULL,
pruning.mode=c("error", "coarse", "fine", "tidy"),
value)
{
@@ -489,7 +489,6 @@ setReplaceMethod("seqinfo", "RangedSummarizedExperiment",
stop("the supplied 'seqinfo' must be a Seqinfo object")
dangling_seqlevels <-
GenomeInfoDb:::getDanglingSeqlevels(x at rowRanges, new2old=new2old,
- force=force,
pruning.mode=pruning.mode,
seqlevels(value))
if (length(dangling_seqlevels) != 0L)
diff --git a/R/findOverlaps-methods.R b/R/findOverlaps-methods.R
index d39afee..b4e4072 100644
--- a/R/findOverlaps-methods.R
+++ b/R/findOverlaps-methods.R
@@ -6,7 +6,7 @@
### findOverlaps
setMethod("findOverlaps", c("RangedSummarizedExperiment", "Vector"),
- function(query, subject, maxgap=0L, minoverlap=1L,
+ function(query, subject, maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
@@ -17,7 +17,7 @@ setMethod("findOverlaps", c("RangedSummarizedExperiment", "Vector"),
)
setMethod("findOverlaps", c("Vector", "RangedSummarizedExperiment"),
- function(query, subject, maxgap=0L, minoverlap=1L,
+ function(query, subject, maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
@@ -29,7 +29,7 @@ setMethod("findOverlaps", c("Vector", "RangedSummarizedExperiment"),
setMethod("findOverlaps", c("RangedSummarizedExperiment",
"RangedSummarizedExperiment"),
- function(query, subject, maxgap=0L, minoverlap=1L,
+ function(query, subject, maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
diff --git a/R/makeSummarizedExperimentFromExpressionSet.R b/R/makeSummarizedExperimentFromExpressionSet.R
index 66d123f..c6655de 100644
--- a/R/makeSummarizedExperimentFromExpressionSet.R
+++ b/R/makeSummarizedExperimentFromExpressionSet.R
@@ -209,6 +209,11 @@ setAs("ExpressionSet", "RangedSummarizedExperiment", function(from)
makeSummarizedExperimentFromExpressionSet(from)
})
+setAs("ExpressionSet", "SummarizedExperiment", function(from)
+{
+ as(makeSummarizedExperimentFromExpressionSet(from), "SummarizedExperiment")
+})
+
setAs("RangedSummarizedExperiment", "ExpressionSet",
function(from)
{
diff --git a/build/vignette.rds b/build/vignette.rds
index a8de930..5f58528 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/SummarizedExperiment.R b/inst/doc/SummarizedExperiment.R
index 716bf4a..b4f6b65 100644
--- a/inst/doc/SummarizedExperiment.R
+++ b/inst/doc/SummarizedExperiment.R
@@ -1,46 +1,46 @@
-## ----style, echo=FALSE, results='asis'-----------------------------------
+## ----style, echo=FALSE, results='asis'-------------------------------------
BiocStyle::markdown()
-## ----include = FALSE-----------------------------------------------------
+## ----include = FALSE-------------------------------------------------------
# download current version of SE diagram
#download.file("https://docs.google.com/feeds/download/drawings/Export?id=18OcDb80FpvSGRYnFl-8vUqwNNLaNHrG1I9SWKHCselo&exportFormat=svg", "SE.svg")
download.file("https://docs.google.com/feeds/download/drawings/Export?id=1kiC8Qlo1mhSnLDqkGiRNPSo6GWn3C2duBszCFbJCB-g&exportFormat=svg", "SE.svg")
-## ---- echo=FALSE---------------------------------------------------------
+## ---- echo=FALSE-----------------------------------------------------------
suppressPackageStartupMessages(library(SummarizedExperiment))
suppressPackageStartupMessages(data(airway, package="airway"))
-## ------------------------------------------------------------------------
+## --------------------------------------------------------------------------
library(SummarizedExperiment)
data(airway, package="airway")
se <- airway
se
-## ----assays, eval = FALSE------------------------------------------------
+## ----assays, eval = FALSE--------------------------------------------------
# assays(se)$counts
-## ----assays_table, echo = FALSE------------------------------------------
+## ----assays_table, echo = FALSE--------------------------------------------
knitr::kable(assays(se)$counts[1:10,])
-## ----rowRanges-----------------------------------------------------------
+## ----rowRanges-------------------------------------------------------------
rowRanges(se)
-## ----colData-------------------------------------------------------------
+## ----colData---------------------------------------------------------------
colData(se)
-## ----columnSubset--------------------------------------------------------
+## ----columnSubset----------------------------------------------------------
# subset for only those samples treated with dexamethasone
se[, se$dex == "trt"]
-## ----metadata------------------------------------------------------------
+## ----metadata--------------------------------------------------------------
metadata(se)
-## ----metadata-formula----------------------------------------------------
+## ----metadata-formula------------------------------------------------------
metadata(se)$formula <- counts ~ dex + albut
metadata(se)
-## ----constructRSE--------------------------------------------------------
+## ----constructRSE----------------------------------------------------------
nrows <- 200
ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
@@ -54,17 +54,17 @@ colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
SummarizedExperiment(assays=list(counts=counts),
rowRanges=rowRanges, colData=colData)
-## ----constructSE---------------------------------------------------------
+## ----constructSE-----------------------------------------------------------
SummarizedExperiment(assays=list(counts=counts), colData=colData)
-## ----2d------------------------------------------------------------------
+## ----2d--------------------------------------------------------------------
# subset the first five transcripts and first three samples
se[1:5, 1:3]
-## ----colDataExtraction---------------------------------------------------
+## ----colDataExtraction-----------------------------------------------------
se[, se$cell == "N61311"]
-## ----getSet--------------------------------------------------------------
+## ----getSet----------------------------------------------------------------
counts <- matrix(1:15, 5, 3, dimnames=list(LETTERS[1:5], LETTERS[1:3]))
dates <- SummarizedExperiment(assays=list(counts=counts),
@@ -73,7 +73,7 @@ dates <- SummarizedExperiment(assays=list(counts=counts),
# Subset all January assays
dates[rowData(dates)$month == "January", ]
-## ----assay_assays--------------------------------------------------------
+## ----assay_assays----------------------------------------------------------
assays(se)
assays(se)[[1]][1:5, 1:5]
@@ -83,13 +83,13 @@ assay(se)[1:5, 1:5]
assay(se, 1)[1:5, 1:5]
-## ----overlap-------------------------------------------------------------
+## ----overlap---------------------------------------------------------------
# Subset for only rows which are in the interval 100,000 to 110,000 of
# chromosome 1
roi <- GRanges(seqnames="1", ranges=100000:1100000)
subsetByOverlaps(se, roi)
-## ----rseSubclass---------------------------------------------------------
+## ----rseSubclass-----------------------------------------------------------
setClass("MyRSESubclass",
contains="RangedSummarizedExperiment",
representation=representation(
diff --git a/inst/doc/SummarizedExperiment.html b/inst/doc/SummarizedExperiment.html
index beb8368..64d9f70 100644
--- a/inst/doc/SummarizedExperiment.html
+++ b/inst/doc/SummarizedExperiment.html
@@ -4,23 +4,29 @@
<head>
-<meta charset="utf-8">
+<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
+
<meta name="author" content="Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès" />
<title>SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest</title>
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+}
+</style>
+
+
-<div id="header">
-<h1 class="title"><em>SummarizedExperiment</em> for Coordinating Experimental Assays, Samples, and Regions of Interest</h1>
-<h4 class="author"><em>Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès</em></h4>
+<div class="container-fluid main-container">
+
+<!-- tabsets -->
+<script>
+$(document).ready(function () {
+ window.buildTabsets("TOC");
+});
+</script>
+
+<!-- code folding -->
+
+
+
+
+
+
+<div class="fluid-row" id="header">
+
+
+
+<h1 class="title toc-ignore"><em>SummarizedExperiment</em> for Coordinating Experimental Assays, Samples, and Regions of Interest</h1>
+<p class="author-name">Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès</p>
<h4 class="date"><em>Revised: 22 June, 2016</em></h4>
+
</div>
<h1>Contents</h1>
@@ -106,7 +171,10 @@ document.addEventListener("DOMContentLoaded", function() {
<p><code>RangedSummarizedExperiment</code> is the child of the <code>SummarizedExperiment</code> class which means that all the methods on <code>SummarizedExperiment</code> also work on a <code>RangedSummarizedExperiment</code>.</p>
<p>The fundamental difference between the two classes is that the rows of a <code>RangedSummarizedExperiment</code> object represent genomic ranges of interest instead of a <code>DataFrame</code> of features. The <code>RangedSummarizedExperiment</code> ranges are described by a <code>GRanges</code> or a <code>GRangesList</code> object, accessible using the <code>rowRanges()</code> function.</p>
<p>The following graphic displays the class geometry and highlights the vertical (column) and horizontal (row) relationships.</p>
-<p><img src="data:image/svg+xml;base64,PD94bWwgdmVyc2lvbj0iMS4wIiBzdGFuZGFsb25lPSJ5ZXMiPz4KCjxzdmcgdmVyc2lvbj0iMS4xIiB2aWV3Qm94PSIwLjAgMC4wIDcwNS41NTM4MDU3NzQyNzgyIDYwMi4xMTU0ODU1NjQzMDQ0IiBmaWxsPSJub25lIiBzdHJva2U9Im5vbmUiIHN0cm9rZS1saW5lY2FwPSJzcXVhcmUiIHN0cm9rZS1taXRlcmxpbWl0PSIxMCIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIiB4bWxuczp4bGluaz0iaHR0cDovL3d3dy53My5vcmcvMTk5OS94bGluayI+PGNsaXBQYXRoIGlkPSJwLjAiPjxwYXRoIGQ9Im0wIDBsNzA1LjU1MzgzIDBsMCA2MDIuMTE1NWwtNzA1LjU1MzgzIDBsMCAtNjAyL [...]
+<div class="figure">
+<img src="data:image/svg+xml;base64,PD94bWwgdmVyc2lvbj0iMS4wIiBzdGFuZGFsb25lPSJ5ZXMiPz4KCjxzdmcgdmVyc2lvbj0iMS4xIiB2aWV3Qm94PSIwLjAgMC4wIDcwNS41NTM4MDU3NzQyNzgyIDYwMi4xMTU0ODU1NjQzMDQ0IiBmaWxsPSJub25lIiBzdHJva2U9Im5vbmUiIHN0cm9rZS1saW5lY2FwPSJzcXVhcmUiIHN0cm9rZS1taXRlcmxpbWl0PSIxMCIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIiB4bWxuczp4bGluaz0iaHR0cDovL3d3dy53My5vcmcvMTk5OS94bGluayI+PGNsaXBQYXRoIGlkPSJwLjAiPjxwYXRoIGQ9Im0wIDBsNzA1LjU1MzgzIDBsMCA2MDIuMTE1NWwtNzA1LjU1MzgzIDBsMCAtNjAyLjEx [...]
+<p class="caption">Summarized Experiment</p>
+</div>
<div id="assays" class="section level2">
<h2><span class="header-section-number">2.1</span> Assays</h2>
<p>The <code>airway</code> package contains an example dataset from an RNA-Seq experiment of read counts per gene for airway smooth muscles. These data are stored in a <code>RangedSummarizedExperiment</code> object which contains 8 different experimental and assays 64,102 gene transcripts.</p>
@@ -527,6 +595,35 @@ subsetByOverlaps(se, roi)</code></pre>
+
+</div>
+
+<script>
+
+// add bootstrap table styles to pandoc tables
+function bootstrapStylePandocTables() {
+ $('tr.header').parent('thead').parent('table').addClass('table table-condensed');
+}
+$(document).ready(function () {
+ bootstrapStylePandocTables();
+});
+
+
+</script>
+
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({
+ "HTML-CSS": {
+ styles: {
+ ".MathJax_Display": {
+ "text-align": "center",
+ padding: "0px 150px 0px 65px",
+ margin: "0px 0px 0.5em"
+ },
+ }
+ }
+ });
+</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
diff --git a/man/findOverlaps-methods.Rd b/man/findOverlaps-methods.Rd
index ef0fe83..f67f052 100644
--- a/man/findOverlaps-methods.Rd
+++ b/man/findOverlaps-methods.Rd
@@ -23,12 +23,12 @@
\usage{
\S4method{findOverlaps}{RangedSummarizedExperiment,Vector}(query, subject,
- maxgap=0L, minoverlap=1L,
+ maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
\S4method{findOverlaps}{Vector,RangedSummarizedExperiment}(query, subject,
- maxgap=0L, minoverlap=1L,
+ maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
diff --git a/man/makeSummarizedExperimentFromExpressionSet.Rd b/man/makeSummarizedExperimentFromExpressionSet.Rd
index 28d175e..10631db 100644
--- a/man/makeSummarizedExperimentFromExpressionSet.Rd
+++ b/man/makeSummarizedExperimentFromExpressionSet.Rd
@@ -5,6 +5,7 @@
\alias{probeRangeMapper}
\alias{geneRangeMapper}
\alias{coerce,ExpressionSet,RangedSummarizedExperiment-method}
+\alias{coerce,ExpressionSet,SummarizedExperiment-method}
\alias{coerce,RangedSummarizedExperiment,ExpressionSet-method}
\alias{coerce,SummarizedExperiment,ExpressionSet-method}
@@ -84,14 +85,15 @@ geneRangeMapper(txDbPackage, key = "ENTREZID")
\examples{
## ---------------------------------------------------------------------
-## GOING FROM ExpressionSet TO RangedSummarizedExperiment
+## GOING FROM ExpressionSet TO SummarizedExperiment
## ---------------------------------------------------------------------
data(sample.ExpressionSet, package="Biobase")
-# 2 equivalent ways of doing the naive coercion
+# naive coercion
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
as(sample.ExpressionSet, "RangedSummarizedExperiment")
+as(sample.ExpressionSet, "SummarizedExperiment")
# using probe range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
@@ -101,7 +103,7 @@ makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
## ---------------------------------------------------------------------
-## GOING FROM RangedSummarizedExperiment TO ExpressionSet
+## GOING FROM SummarizedExperiment TO ExpressionSet
## ---------------------------------------------------------------------
example(RangedSummarizedExperiment) # to create 'rse'
--
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