DASiR 1.12.0
Ricard Illa
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DASiR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DASiR
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* checking for file ‘DASiR/DESCRIPTION’ ... OK
* preparing ‘DASiR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
version 3.3
DASiR-package package:DASiR R Documentation
_D_i_s_t_r_i_b_u_t_e_d _A_n_n_o_t_a_t_i_o_n _S_y_s_t_e_m _i_n _R
_D_e_s_c_r_i_p_t_i_o_n:
R package for programmatic retrieval of information from DAS
servers
_D_e_t_a_i_l_s:
Package: DASiR
Type: Package
License: LGPL(>= 3)
Distributed Annotation System (DAS) is a protocol for information
exchange between a server and a client. Is widely used in
bioinformatics and the most important repositories include a DAS
server parallel to their main front-end.
DAS uses XML and HTTP protocols, so the requirements are much less
than using MySQL or BioMart based alternatives.
This package provides a convenient R-DAS interface to
programmatically access DAS servers available from your network.
It supports only the basic features of DAS 1.6 protocol (DAS/2 is
not supported) but these should be enough for most of the users.
Despite a large number (>1200 according official numbers on
February 2013) are available, this package is designed with
range-features (neither coverages nor sequences). DAS also
supports querying genomic sequences and protein structures, but
there are already better ways to access such static data in R.
In order to start with this package, you can give a look to basic
metadata functions in ‘getDas-functions’ man page and to the main
functions ‘getDasFeature, getDasSequence, getDasStructure’.
Basic support for graphical representation is also provided
through ‘plotFeatures’.
As a final consideration, you should have in mind that public
available DAS servers are a valuable service and you should give
them a reasonable use. Please, don't overload the servers with
many or large queries.
_A_u_t_h_o_r(_s):
Oscar Flores <oflores@mmb.pcb.ub.es>
Anna Mantsoki <anna.mantsoki@bsc.es>
_R_e_f_e_r_e_n_c_e_s:
BioDas Wiki - http://www.biodas.org/
DAS 1.6 Specification -
http://www.ebi.ac.uk/˜aj/1.6_draft7/documents/spec.html
DAS servers catalog - http://www.dasregistry.org/
_E_x_a_m_p_l_e_s:
setDasServer(server="http://www.ensembl.org/das")
print(getDasServer())
# See the sources (supported organisms)
sources <- getDasSource()
head(sources)
dsn_sources <- getDasDsn()
head(dsn_sources)
# Notice that sources returns more information but we need the source ID
# given by getDasDsn, that corresponds to getDasSource$title in this
# server.
# The server we are quering is a genomic sequence server, so no gene
# information nor structure is available here
# Let's see what this sever supports for SCerevisiae
source <- "Saccharomyces_cerevisiae.EF4.reference"
# das1:entry_points das1:sequence das1:features
sources[grep(source, sources$title), ]
# Ask for the entries
entries <- getDasEntries(source)
head(entries)
# Retrive first 1000nts in the beginning of chromosomes I and II
range <- GRanges(c("I", "II"), IRanges(start=1, end=1000))
seq <- getDasSequence(source, range, class="DNAStringSet")
# Server supports features, but not types...
types <- getDasTypes(source)
# Server returns null... So we will perform a query without types
print(types)
# Let's see which features is returning the server
features <- getDasFeature(source, range, NULL)
print(features)
# Features here are not genomic features (like genes), this is only
# sequence info
# In the webpage http://www.dasregistry.org/listSources.jsp
# We can see all the registred DAS servers and the information they provide
# Remember that DASiR is only an interface to DAS servers! You should know
# what the server you are querying contains and if it supports your desired
# features!
# Now let's retrieve genes in that region from another source
# This is UCSC Genome browser, which has access to all the features
# displayed in the webpage
setDasServer(server="http://genome.ucsc.edu/cgi-bin/das")
# Notice that id now changes, we can retrieve it from getDasDsn()
source <- "sacCer3"
# Retrieve the types
types <- getDasTypes(source)
# We want the official genes from 'sdgGene' and the ENSEMBL predicted genes
# from 'ensGene'
features <- getDasFeature(source, range, c("sgdGene","ensGene"))
print(features)
# We obtain a total of 4 genes, 2 in chromosome I and 2 in chromosome II
# Notice each gene appears 2 times, one as a sgdGene and another as ensGene
# Now plot the features (but only from one range at a time!)
# Notice that with the default parameters each feature will appear with a
# different color
plotFeatures(features[features$segment.range == 1,])
DAS server for this session is: http://genome.ucsc.edu/cgi-bin/das
Querying url: http://genome.ucsc.edu/cgi-bin/das/dsn
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/entry_points
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/types
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/features
DAS server for this session is: http://vega.sanger.ac.uk/das
Quering url: http://vega.sanger.ac.uk/das/Homo_sapiens.VEGA51.reference/sequence
Error: could not find function "xmlStructuredStop"...
Quering url: http://vega.sanger.ac.uk/das/Homo_sapiens.VEGA51.reference/sequence
Error: could not find function "xmlStructuredStop"...
DAS server for this session is: http://das.cathdb.info/das
Quering url: http://das.cathdb.info/das/cath_pdb/structure?query=1hck
Warning in download.file(url, destfile = tf, quiet = TRUE) :
cannot open URL 'http://das.cathdb.info/das/cath_pdb/structure?query=1hck': HTTP status was '404 Not Found'
Error: processing vignette 'DASiR.Rnw' failed with diagnostics:
chunk 9 (label = getDasStructure)
Error in download.file(url, destfile = tf, quiet = TRUE) :
cannot open URL 'http://das.cathdb.info/das/cath_pdb/structure?query=1hck'
Execution halted