[Bioc-devel] GRanges to VRanges coercion
Hi Valerie, hi Michael,
I find myself frequently moving back and forth between data.frames, GRanges
and VRanges objects.
The makeGRangesFromDataFrame function from the GenomicRanges makes the
coercion between the former straightforward, but I couldn't find anything
similar for the second step, coercsion from GRanges to VRanges.
There is a coercion method defined in the GenomicRanges package:
getMethod(coerce, c(GRanges, VRanges))
Method Definition:
function (from, to = VRanges, strict = TRUE)
{
obj - new(VRanges)
as(obj, GRanges) - from
obj
}
environment: namespace:GenomicRanges
Signatures:
from to
target GRanges VRanges
defined GRanges VRanges
but I haven't been able to get it to work (or find where it is documented).
The source code shown above doesn't indicate how the coercion method would
check for the presence of required / optional VRanges columns, e.g. 'ref',
'alt', 'altDepth', etc.
Would it be useful to add an explicit makeVRangesFromGRanges function to
the VariantAnnotation package ( and / or the corresponding coercion method)
?
Then it would be easy to go from a data.frame to a VRanges object, e.g. as
in this pseudocode:
makeVRangesFromGRanges(
makeGRangesFromDataFrame( data.frame )
)
You can find a first attempt at implementing the
makeVRangesFromGRanges function
here https://gist.github.com/tomsing1/bf917b1b48afb952e1c5, which you are
welcome to use / modify if you find it useful.
If this functionality should already be available, I'd be happy to learn
about that, too !
Thank you,
Thomas
SessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] VariantAnnotation_1.12.9 Rsamtools_1.18.2 Biostrings_2.34.1
XVector_0.6.0GenomicRanges_1.18.4
[6] GenomeInfoDb_1.2.4 IRanges_2.0.1S4Vectors_0.4.0
BiocGenerics_0.12.1 BiocInstaller_1.16.1
[11] roxygen2_4.1.0 devtools_1.7.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.1base64enc_0.1-2 BatchJobs_1.5
BBmisc_1.9 Biobase_2.26.0
[6] BiocParallel_1.0.3 biomaRt_2.22.0 bitops_1.0-6
brew_1.0-6 BSgenome_1.34.1
[11] checkmate_1.5.1 codetools_0.2-10DBI_0.3.1
digest_0.6.8fail_1.2
[16] foreach_1.4.2 GenomicAlignments_1.2.1 GenomicFeatures_1.18.3
iterators_1.0.7 Rcpp_0.11.4
[21] RCurl_1.95-4.5 RSQLite_1.0.0 rtracklayer_1.26.2
sendmailR_1.2-1 stringr_0.6.2
[26] tools_3.1.2 XML_3.98-1.1zlibbioc_1.12.0
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[Bioc-devel] Fwd: readGAlignmentsFromBam function
-- Forwarded message -- From: Karolis Uziela karolis.uzi...@scilifelab.se Date: Feb 19, 2015 9:22 AM Subject: readGAlignmentsFromBam function To: Michael Lawrence lawrence.mich...@gene.com Cc: bioconduc...@r-project.org bioconduc...@r-project.org Hi, I have looked at R check results for the devel version of Bioconductor and I noticed that the package I developed (prebs) gives this warning: Warning: 'readGAlignmentsFromBam' is deprecated. What is the new function that should be used instead of readGAlignmentsFromBam (GenomicAlignments package)? Do the changes affect readGAlignmentPairs function, too? Regards, Karolis -- Karolis Uziela PhD student Science for Life Laboratory Box 1031 17121 Solna, Sweden Mob. +46 729 120 395 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GEOquery Warnings When Reading SOFT File
Hi Dario, This isn't the right forum for your question (this listserv is for development of packages, not questions about existing packages), so you should ask on the support site. Best, Jim On Thu, Feb 19, 2015 at 1:00 AM, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: library(GEOquery) gastricChina - getGEO(GSE65801, GSEMatrix = FALSE) Generates warnings head(warnings(), 1) Warning message: In readLines(con, n = chunksize) : seek on a gzfile connection returned an internal error Does it affect the correctness of the imported data ? Also, experimentData(gastricChina) gives an empty result Experiment data Experimenter name: Laboratory: Contact information: Title: URL: PMIDs: No abstract available. whereas some of the fields are filled in on the webpage. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fwd: readGAlignmentsFromBam function
Hi Karolis, Please use the bioc-devel mailing list (to which you should be subscribed) to ask this type of question. If you manually run the example in your package (using BioC devel, which requires R-3.2), you'll get: prebs_values - calc_prebs(bam_files, manufacturer_cdf_mapping) Inferred name for CDF package: HGU133Plus2_mapping.txt - hgu133plus2cdf [1] Finished: /home/hpages/R/R-3.2.r67773/library/prebsdata/sample_bam_files/input1.bam [1] Finished: /home/hpages/R/R-3.2.r67773/library/prebsdata/sample_bam_files/input2.bam Note: Some probe IDs contain duplicates. Estimated values for Bayesian prior: Alpha=1e-04 Beta=0.0136640101662362 Note: 41457 probe sequences are missing in _mapping.txt file. Normalizing Calculating Expression Warning messages: 1: 'readGAlignmentsFromBam' is deprecated. Use 'readGAlignments' instead. See help(Deprecated) 2: 'readGAlignmentsFromBam' is deprecated. Use 'readGAlignments' instead. See help(Deprecated) Hope this helps. Too bad 'R CMD check' truncates the deprecation message :-/ Cheers, H. On 02/19/2015 01:15 PM, Michael Lawrence wrote: -- Forwarded message -- From: Karolis Uziela karolis.uzi...@scilifelab.se Date: Feb 19, 2015 9:22 AM Subject: readGAlignmentsFromBam function To: Michael Lawrence lawrence.mich...@gene.com Cc: bioconduc...@r-project.org bioconduc...@r-project.org Hi, I have looked at R check results for the devel version of Bioconductor and I noticed that the package I developed (prebs) gives this warning: Warning: 'readGAlignmentsFromBam' is deprecated. What is the new function that should be used instead of readGAlignmentsFromBam (GenomicAlignments package)? Do the changes affect readGAlignmentPairs function, too? Regards, Karolis -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
