[med-svn] [r-bioc-annotationhub] 01/05: New upstream version 2.8.2
Andreas Tille
tille at debian.org
Fri Sep 22 11:50:37 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-annotationhub.
commit d00ac23929c0df898a6c5a5525b63b88cca33144
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 22 13:42:17 2017 +0200
New upstream version 2.8.2
---
DESCRIPTION | 4 +-
R/Hub-utils.R | 2 +-
inst/doc/AnnotationHub-HOWTO.html | 60 +++++++++++++-------------
inst/doc/AnnotationHub.html | 90 +++++++++++++++++++--------------------
4 files changed, 78 insertions(+), 78 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 28925ea..a24bbfd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: AnnotationHub
Type: Package
Title: Client to access AnnotationHub resources
-Version: 2.8.1
+Version: 2.8.2
Authors at R:
c(person("Martin", "Morgan", email="martin.morgan at roswellpark.org",
role="cre"),
@@ -40,4 +40,4 @@ Author: Martin Morgan [cre],
Marc Carlson [ctb],
Dan Tenenbaum [ctb],
Sonali Arora [ctb]
-Packaged: 2017-05-03 23:27:00 UTC; biocbuild
+Packaged: 2017-06-10 23:23:37 UTC; biocbuild
diff --git a/R/Hub-utils.R b/R/Hub-utils.R
index 76965db..de4d273 100644
--- a/R/Hub-utils.R
+++ b/R/Hub-utils.R
@@ -93,7 +93,7 @@
stop("length(biocversion) must == 1")
yaml <- content(GET("http://bioconductor.org/config.yaml"),
- encoding="UTF8", as="text")
+ encoding="UTF-8", as="text")
obj <- yaml.load(yaml)
release_dates <- obj$release_dates
version_date <- release_dates[biocversion == names(release_dates)]
diff --git a/inst/doc/AnnotationHub-HOWTO.html b/inst/doc/AnnotationHub-HOWTO.html
index 8756310..1076cdd 100644
--- a/inst/doc/AnnotationHub-HOWTO.html
+++ b/inst/doc/AnnotationHub-HOWTO.html
@@ -77,7 +77,7 @@ document.addEventListener("DOMContentLoaded", function() {
links[i].target = '_blank';
});
</script>
-<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: Sun Jun 28 10:41:23 2015<br /> <strong>Compiled</strong>: Wed May 3 19:25:52 2017</p>
+<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: Sun Jun 28 10:41:23 2015<br /> <strong>Compiled</strong>: Sat Jun 10 19:22:37 2017</p>
<div id="accessing-genome-scale-data" class="section level1">
<h1><span class="header-section-number">1</span> Accessing Genome-Scale Data</h1>
<div id="non-model-organism-gene-annotations" class="section level2">
@@ -87,27 +87,27 @@ document.addEventListener("DOMContentLoaded", function() {
ah <- AnnotationHub()</code></pre>
<pre><code>## snapshotDate(): 2017-04-25</code></pre>
<pre class="r"><code>query(ah, "OrgDb")</code></pre>
-<pre><code>## AnnotationHub with 19 records
+<pre><code>## AnnotationHub with 940 records
## # snapshotDate(): 2017-04-25
## # $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
-## # $species: Escherichia coli, Anopheles gambiae, Arabidopsis thaliana, Bos taurus, Caenorhabditi...
+## # $species: Escherichia coli, Acanthamoeba castellanii_str._Neff, Acanthisitta chloris, Acetobac...
## # $rdataclass: OrgDb
## # additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
## # rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH53757"]]'
##
-## title
-## AH53757 | org.Ag.eg.db.sqlite
-## AH53758 | org.At.tair.db.sqlite
-## AH53759 | org.Bt.eg.db.sqlite
-## AH53760 | org.Cf.eg.db.sqlite
-## AH53761 | org.Gg.eg.db.sqlite
-## ... ...
-## AH53771 | org.Ce.eg.db.sqlite
-## AH53772 | org.Xl.eg.db.sqlite
-## AH53773 | org.Sc.sgd.db.sqlite
-## AH53774 | org.Dr.eg.db.sqlite
-## AH53775 | org.Pf.plasmo.db.sqlite</code></pre>
+## title
+## AH53757 | org.Ag.eg.db.sqlite
+## AH53758 | org.At.tair.db.sqlite
+## AH53759 | org.Bt.eg.db.sqlite
+## AH53760 | org.Cf.eg.db.sqlite
+## AH53761 | org.Gg.eg.db.sqlite
+## ... ...
+## AH56649 | org.Thermoplasmatales_archaeon_BRNA1.eg.sqlite
+## AH56650 | org.Ignicoccus_hospitalis_KIN4|I.eg.sqlite
+## AH56651 | org.Desulfurococcus_amylolyticus_DSM_16532.eg.sqlite
+## AH56652 | org.Pandoravirus_dulcis.eg.sqlite
+## AH56653 | org.Methanocaldococcus_infernus_ME.eg.sqlite</code></pre>
<pre class="r"><code>orgdb <- query(ah, "OrgDb")[[1]] </code></pre>
<pre><code>## loading from cache '/home/biocbuild//.AnnotationHub/60495'</code></pre>
<p>The object returned by AnnotationHub is directly usable with the <code>select()</code> interface, e.g., to discover the available keytypes for querying the object, the columns that these keytypes can map to, and finally selecting the SYMBOL and GENENAME corresponding to the first 6 ENTREZIDs</p>
@@ -447,8 +447,8 @@ chainfiles</code></pre>
<p>Perform the liftOver operation using <code>rtracklayer::liftOver()</code>:</p>
<pre class="r"><code>library(rtracklayer)
gr38 <- liftOver(peaks, chain)</code></pre>
-<pre><code>## Warning: closing unused connection 6 (/tmp/Rtmp4CdWfE/file42086a9c284e)</code></pre>
-<pre><code>## Warning: closing unused connection 5 (/tmp/Rtmp4CdWfE/file42081f40ea18)</code></pre>
+<pre><code>## Warning: closing unused connection 6 (/tmp/Rtmprm2Zka/file28c86026b3d3)</code></pre>
+<pre><code>## Warning: closing unused connection 5 (/tmp/Rtmprm2Zka/file28c84dffa6ed)</code></pre>
<p>This returns a <em>GRangeslist</em>; update the genome of the result to get the final result</p>
<pre class="r"><code>genome(gr38) <- "hg38"
gr38</code></pre>
@@ -682,27 +682,27 @@ overlap[idx]</code></pre>
##
## other attached packages:
## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.0
-## [3] rtracklayer_1.36.1 VariantAnnotation_1.22.0
-## [5] SummarizedExperiment_1.6.1 DelayedArray_0.2.0
+## [3] rtracklayer_1.36.3 VariantAnnotation_1.22.1
+## [5] SummarizedExperiment_1.6.3 DelayedArray_0.2.7
## [7] matrixStats_0.52.2 Rsamtools_1.28.0
-## [9] Biostrings_2.44.0 XVector_0.16.0
-## [11] GenomicFeatures_1.28.0 AnnotationDbi_1.38.0
-## [13] Biobase_2.36.2 GenomicRanges_1.28.1
-## [15] GenomeInfoDb_1.12.0 IRanges_2.10.0
-## [17] S4Vectors_0.14.0 AnnotationHub_2.8.1
+## [9] Biostrings_2.44.1 XVector_0.16.0
+## [11] GenomicFeatures_1.28.3 AnnotationDbi_1.38.1
+## [13] Biobase_2.36.2 GenomicRanges_1.28.3
+## [15] GenomeInfoDb_1.12.2 IRanges_2.10.2
+## [17] S4Vectors_0.14.3 AnnotationHub_2.8.2
## [19] BiocGenerics_0.22.0 BiocStyle_2.4.0
##
## loaded via a namespace (and not attached):
-## [1] Rcpp_0.12.10 compiler_3.4.0 BiocInstaller_1.26.0
+## [1] Rcpp_0.12.11 compiler_3.4.0 BiocInstaller_1.26.0
## [4] bitops_1.0-6 tools_3.4.0 zlibbioc_1.22.0
-## [7] biomaRt_2.32.0 digest_0.6.12 lattice_0.20-35
+## [7] biomaRt_2.32.1 digest_0.6.12 lattice_0.20-35
## [10] RSQLite_1.1-2 evaluate_0.10 memoise_1.1.0
## [13] Matrix_1.2-10 shiny_1.0.3 DBI_0.6-1
## [16] curl_2.6 yaml_2.1.14 GenomeInfoDbData_0.99.0
-## [19] httr_1.2.1 stringr_1.2.0 knitr_1.15.1
-## [22] grid_3.4.0 rprojroot_1.2 R6_2.2.0
-## [25] BiocParallel_1.10.1 XML_3.98-1.6 rmarkdown_1.5
-## [28] magrittr_1.5 GenomicAlignments_1.12.0 backports_1.0.5
+## [19] httr_1.2.1 stringr_1.2.0 knitr_1.16
+## [22] grid_3.4.0 rprojroot_1.2 R6_2.2.1
+## [25] BiocParallel_1.10.1 XML_3.98-1.7 rmarkdown_1.5
+## [28] magrittr_1.5 GenomicAlignments_1.12.1 backports_1.1.0
## [31] htmltools_0.3.6 mime_0.5 interactiveDisplayBase_1.14.0
## [34] xtable_1.8-2 httpuv_1.3.3 stringi_1.1.5
## [37] RCurl_1.95-4.8</code></pre>
diff --git a/inst/doc/AnnotationHub.html b/inst/doc/AnnotationHub.html
index dc94e47..95b3998 100644
--- a/inst/doc/AnnotationHub.html
+++ b/inst/doc/AnnotationHub.html
@@ -74,7 +74,7 @@ document.addEventListener("DOMContentLoaded", function() {
links[i].target = '_blank';
});
</script>
-<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: 27 May, 2016<br /> <strong>Compiled</strong>: Wed May 3 19:26:51 2017</p>
+<p><strong>Package</strong>: <em><a href="http://bioconductor.org/packages/AnnotationHub">AnnotationHub</a></em><br /> <strong>Authors</strong>: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]<br /> <strong>Modified</strong>: 27 May, 2016<br /> <strong>Compiled</strong>: Sat Jun 10 19:23:30 2017</p>
<p>The <code>AnnotationHub</code> server provides easy <em>R / Bioconductor</em> access to large collections of publicly available whole genome resources, e.g,. ENSEMBL genome fasta or gtf files, UCSC chain resources, ENCODE data tracks at UCSC, etc.</p>
<div id="annotationhub-objects" class="section level1">
<h1><span class="header-section-number">1</span> AnnotationHub objects</h1>
@@ -86,28 +86,28 @@ document.addEventListener("DOMContentLoaded", function() {
<p>Now at this point you have already done everything you need in order to start retrieving annotations. For most operations, using the <code>AnnotationHub</code> object should feel a lot like working with a familiar <code>list</code> or <code>data.frame</code>.</p>
<p>Lets take a minute to look at the show method for the hub object ah</p>
<pre class="r"><code>ah</code></pre>
-<pre><code>## AnnotationHub with 39213 records
+<pre><code>## AnnotationHub with 40134 records
## # snapshotDate(): 2017-04-25
-## # $dataprovider: BroadInstitute, Ensembl, UCSC, Haemcode, Inparanoid8, ...
+## # $dataprovider: BroadInstitute, Ensembl, UCSC, Haemcode, ftp://ftp.ncb...
## # $species: Homo sapiens, Mus musculus, Bos taurus, Pan troglodytes, Da...
-## # $rdataclass: GRanges, BigWigFile, FaFile, TwoBitFile, ChainFile, Rle,...
+## # $rdataclass: GRanges, BigWigFile, FaFile, TwoBitFile, ChainFile, OrgD...
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## # tags, rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH2"]]'
##
-## title
-## AH2 | Ailuropoda_melanoleuca.ailMel1.69.dna.toplevel.fa
-## AH3 | Ailuropoda_melanoleuca.ailMel1.69.dna_rm.toplevel.fa
-## AH4 | Ailuropoda_melanoleuca.ailMel1.69.dna_sm.toplevel.fa
-## AH5 | Ailuropoda_melanoleuca.ailMel1.69.ncrna.fa
-## AH6 | Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa
-## ... ...
-## AH54627 | Xiphophorus_maculatus.Xipmac4.4.2.cdna.all.2bit
-## AH54628 | Xiphophorus_maculatus.Xipmac4.4.2.dna.toplevel.2bit
-## AH54629 | Xiphophorus_maculatus.Xipmac4.4.2.dna_rm.toplevel.2bit
-## AH54630 | Xiphophorus_maculatus.Xipmac4.4.2.dna_sm.toplevel.2bit
-## AH54631 | Xiphophorus_maculatus.Xipmac4.4.2.ncrna.2bit</code></pre>
+## title
+## AH2 | Ailuropoda_melanoleuca.ailMel1.69.dna.toplevel.fa
+## AH3 | Ailuropoda_melanoleuca.ailMel1.69.dna_rm.toplevel.fa
+## AH4 | Ailuropoda_melanoleuca.ailMel1.69.dna_sm.toplevel.fa
+## AH5 | Ailuropoda_melanoleuca.ailMel1.69.ncrna.fa
+## AH6 | Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa
+## ... ...
+## AH56649 | org.Thermoplasmatales_archaeon_BRNA1.eg.sqlite
+## AH56650 | org.Ignicoccus_hospitalis_KIN4|I.eg.sqlite
+## AH56651 | org.Desulfurococcus_amylolyticus_DSM_16532.eg.sqlite
+## AH56652 | org.Pandoravirus_dulcis.eg.sqlite
+## AH56653 | org.Methanocaldococcus_infernus_ME.eg.sqlite</code></pre>
<p>You can see that it gives you an idea about the different types of data that are present inside the hub. You can see where the data is coming from (dataprovider), as well as what species have samples present (species), what kinds of R data objects could be returned (rdataclass). We can take a closer look at all the kinds of data providers that are available by simply looking at the contents of dataprovider as if it were the column of a data.frame object like this:</p>
<pre class="r"><code>unique(ah$dataprovider)</code></pre>
<pre><code>## [1] "Ensembl"
@@ -170,7 +170,7 @@ dm</code></pre>
<pre class="r"><code>df <- mcols(dm)</code></pre>
<p>By default the show method will only display the first 5 and last 5 rows. There are already thousands of records present in the hub.</p>
<pre class="r"><code>length(ah)</code></pre>
-<pre><code>## [1] 39213</code></pre>
+<pre><code>## [1] 40134</code></pre>
<p>Lets look at another example, where we pull down only Inparanoid8 data from the hub and use subset to return a smaller base object (here we are finding cases where the genome column is set to panda).</p>
<pre class="r"><code>ahs <- query(ah, c('inparanoid8', 'ailuropoda'))
ahs</code></pre>
@@ -251,28 +251,28 @@ ahs</code></pre>
<p>When you create the <code>AnnotationHub</code> object, it will set up the object for you with some default settings. See <code>?AnnotationHub</code> for ways to customize the hub source, the local cache, and other instance-specific options, and <code>?getAnnotationHubOption</code> to get or set package-global options for use across sessions.</p>
<p>If you look at the object you will see some helpful information about it such as where the data is cached and where online the hub server is set to.</p>
<pre class="r"><code>ah</code></pre>
-<pre><code>## AnnotationHub with 39213 records
+<pre><code>## AnnotationHub with 40134 records
## # snapshotDate(): 2017-04-25
-## # $dataprovider: BroadInstitute, Ensembl, UCSC, Haemcode, Inparanoid8, ...
+## # $dataprovider: BroadInstitute, Ensembl, UCSC, Haemcode, ftp://ftp.ncb...
## # $species: Homo sapiens, Mus musculus, Bos taurus, Pan troglodytes, Da...
-## # $rdataclass: GRanges, BigWigFile, FaFile, TwoBitFile, ChainFile, Rle,...
+## # $rdataclass: GRanges, BigWigFile, FaFile, TwoBitFile, ChainFile, OrgD...
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## # tags, rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH2"]]'
##
-## title
-## AH2 | Ailuropoda_melanoleuca.ailMel1.69.dna.toplevel.fa
-## AH3 | Ailuropoda_melanoleuca.ailMel1.69.dna_rm.toplevel.fa
-## AH4 | Ailuropoda_melanoleuca.ailMel1.69.dna_sm.toplevel.fa
-## AH5 | Ailuropoda_melanoleuca.ailMel1.69.ncrna.fa
-## AH6 | Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa
-## ... ...
-## AH54627 | Xiphophorus_maculatus.Xipmac4.4.2.cdna.all.2bit
-## AH54628 | Xiphophorus_maculatus.Xipmac4.4.2.dna.toplevel.2bit
-## AH54629 | Xiphophorus_maculatus.Xipmac4.4.2.dna_rm.toplevel.2bit
-## AH54630 | Xiphophorus_maculatus.Xipmac4.4.2.dna_sm.toplevel.2bit
-## AH54631 | Xiphophorus_maculatus.Xipmac4.4.2.ncrna.2bit</code></pre>
+## title
+## AH2 | Ailuropoda_melanoleuca.ailMel1.69.dna.toplevel.fa
+## AH3 | Ailuropoda_melanoleuca.ailMel1.69.dna_rm.toplevel.fa
+## AH4 | Ailuropoda_melanoleuca.ailMel1.69.dna_sm.toplevel.fa
+## AH5 | Ailuropoda_melanoleuca.ailMel1.69.ncrna.fa
+## AH6 | Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa
+## ... ...
+## AH56649 | org.Thermoplasmatales_archaeon_BRNA1.eg.sqlite
+## AH56650 | org.Ignicoccus_hospitalis_KIN4|I.eg.sqlite
+## AH56651 | org.Desulfurococcus_amylolyticus_DSM_16532.eg.sqlite
+## AH56652 | org.Pandoravirus_dulcis.eg.sqlite
+## AH56653 | org.Methanocaldococcus_infernus_ME.eg.sqlite</code></pre>
<p>By default the <code>AnnotationHub</code> object is set to the latest <code>snapshotData</code> and a snapshot version that matches the version of <em>Bioconductor</em> that you are using. You can also learn about these data with the appropriate methods.</p>
<pre class="r"><code>snapshotDate(ah)</code></pre>
<pre><code>## [1] "2017-04-25"</code></pre>
@@ -343,32 +343,32 @@ txdb <- loadDb("/locationToFile/mytxdb.sqlite")</code></pre>
##
## other attached packages:
## [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.0
-## [3] rtracklayer_1.36.1 VariantAnnotation_1.22.0
-## [5] SummarizedExperiment_1.6.1 DelayedArray_0.2.0
+## [3] rtracklayer_1.36.3 VariantAnnotation_1.22.1
+## [5] SummarizedExperiment_1.6.3 DelayedArray_0.2.7
## [7] matrixStats_0.52.2 Rsamtools_1.28.0
-## [9] Biostrings_2.44.0 XVector_0.16.0
-## [11] GenomicFeatures_1.28.0 AnnotationDbi_1.38.0
-## [13] Biobase_2.36.2 GenomicRanges_1.28.1
-## [15] GenomeInfoDb_1.12.0 IRanges_2.10.0
-## [17] S4Vectors_0.14.0 AnnotationHub_2.8.1
+## [9] Biostrings_2.44.1 XVector_0.16.0
+## [11] GenomicFeatures_1.28.3 AnnotationDbi_1.38.1
+## [13] Biobase_2.36.2 GenomicRanges_1.28.3
+## [15] GenomeInfoDb_1.12.2 IRanges_2.10.2
+## [17] S4Vectors_0.14.3 AnnotationHub_2.8.2
## [19] BiocGenerics_0.22.0 BiocStyle_2.4.0
##
## loaded via a namespace (and not attached):
-## [1] Rcpp_0.12.10 compiler_3.4.0
+## [1] Rcpp_0.12.11 compiler_3.4.0
## [3] BiocInstaller_1.26.0 bitops_1.0-6
## [5] tools_3.4.0 zlibbioc_1.22.0
-## [7] biomaRt_2.32.0 digest_0.6.12
+## [7] biomaRt_2.32.1 digest_0.6.12
## [9] lattice_0.20-35 RSQLite_1.1-2
## [11] evaluate_0.10 memoise_1.1.0
## [13] Matrix_1.2-10 shiny_1.0.3
## [15] DBI_0.6-1 curl_2.6
## [17] yaml_2.1.14 GenomeInfoDbData_0.99.0
## [19] httr_1.2.1 stringr_1.2.0
-## [21] knitr_1.15.1 grid_3.4.0
-## [23] rprojroot_1.2 R6_2.2.0
-## [25] BiocParallel_1.10.1 XML_3.98-1.6
+## [21] knitr_1.16 grid_3.4.0
+## [23] rprojroot_1.2 R6_2.2.1
+## [25] BiocParallel_1.10.1 XML_3.98-1.7
## [27] rmarkdown_1.5 magrittr_1.5
-## [29] GenomicAlignments_1.12.0 backports_1.0.5
+## [29] GenomicAlignments_1.12.1 backports_1.1.0
## [31] htmltools_0.3.6 mime_0.5
## [33] interactiveDisplayBase_1.14.0 xtable_1.8-2
## [35] httpuv_1.3.3 stringi_1.1.5
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-annotationhub.git
More information about the debian-med-commit
mailing list