Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > *From:* Bioc-devel on behalf of > Kern, Lori via Bioc-devel > *Sent:* Friday, April 5, 2024 8:15 AM &

[Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

hi, I'm getting duplicated entries when loading **offline** previously cached ExperimentHub resources. This code reproduces the problem: 1. If in a fresh empty cache of ExperimentHub I download 9 resources through the gDNAinRNAseqData package: library(gDNAinRNAseqData) bamfiles <-

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

hi, related to this, I found recently the problem that the TxDb.Hsapiens.UCSC.hg38.knownGene package contains only a few of the RN7SL (RNA component of signal recognition particle 7SL) genes and I suspect the problem is that on the one hand UCSC currently provides the 'knownGene' track based

Re: [Bioc-devel] issue to open a file from UCSC

thz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 ___ Bioc

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

ully turn green on > kunpeng2 today: > https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx > > Best, > > H. > > On 10/23/23 23:29, Robert Castelo wrote: >> >> Hervé, Martin, >> >> Thank you so much, atena builds and checks cleanly now on k

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

2023 at 7:26 PM Hervé Pagès >> wrote: >> >> Hi Robert, >> >> There's the possibility that some of these BAM files got >> corrupted when >> downloaded to kunpeng2 local cache. >> >> @Martin Gregorov: Would you be able to try

[Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

of the other platforms. Should we do anything about this? Thanks! robert. -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514

Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db

__     Bioc-devel@r-project.org mailing list     https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Re

Re: [Bioc-devel] Empty DataFrame Causes SummarizedExperiment Constructor Error

ist https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514

Re: [Bioc-devel] httr::GET() problem downloading a ExperimentHub resource

les have Content-Encoding: gzip, > but there is no Content-Encoding tag on the BAM file above. I guess > BAM files are (some flavor of) gzip (?), but maybe this is confusing > the R curl library… > > Martin > > *From: *Robert Castelo > *Date: *Wednesday, March 29, 2023 at 4

Re: [Bioc-devel] httr::GET() problem downloading a ExperimentHub resource

ed writing received data to disk/application > > I notice the index file (extension .bai) works; do other BAM files > work, too? > > Martin > > *From: *Bioc-devel on behalf of > Robert Castelo > *Date: *Wednesday, March 29, 2023 at 1:18 PM > *To: *bioc-devel@r-proj

[Bioc-devel] httr::GET() problem downloading a ExperimentHub resource

hi, we recently added a few new ExperimentHub resources, consisting of BAM files and their corresponding BAI files and hosted in my own server. while it seems that they are accessible, they cannot be downloaded through the ExperimentHub API. the minimum example reproducing the problem is this

Re: [Bioc-devel] Unable to Push Error

n. Thank you for your time, Max [[alternative HTML version deleted]] _______ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted

Re: [Bioc-devel] missing GenomicScores platform availability shield for release

Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > -------- > *From:* Bioc-devel on behalf of > Robert Castelo > *Sent:* Wednes

[Bioc-devel] missing GenomicScores platform availability shield for release

hi, the platform availability shield for the release version of GenomicScores pointing here: https://bioconductor.org/shields/availability/release/GenomicScores.svg is missing, if i look up the same shield for another of my packages, it's there:

Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

c-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain te

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

ica de privacidad en www.isglobal.org <http://www.isglobal.org/>. [[alternative HTML version deleted]] ___________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor D

Re: [Bioc-devel] How to update an experiment data package

s > > Elm & Carlton Streets > > Buffalo, New York 14263 > > -------- > *From:* Bioc-devel on behalf of > Robert Castelo > *Sent:* Thursday, February 4, 2021 2:03 PM > *To:* bioc-devel@r-project.org > *

[Bioc-devel] How to update an experiment data package

Hi, I'd like to update the experiment data package https://bioconductor.org/packages/GSVAdata but i haven't been able to find instructions in the Bioconductor website. how do i proceed? thanks! robert. -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences

Re: [Bioc-devel] glitches with releaseName() and seqlevelsStyle()

Hi Hervé, On 02/09/2020 21:44, Pages, Herve wrote: Hi Robert, On 9/2/20 11:12, Robert Castelo wrote: hi, i've found the following glitches with 'releaseName()' and 'seqlevelsStyle()', i guess due to recent changes in BSgenome and GenomeInfoDb, which is why i'm cc'ing Hervé

[Bioc-devel] glitches with releaseName() and seqlevelsStyle()

hi, i've found the following glitches with 'releaseName()' and 'seqlevelsStyle()', i guess due to recent changes in BSgenome and GenomeInfoDb, which is why i'm cc'ing Hervé ;) ===BioC release 3.11 everything OK= library(BSgenome.Hsapiens.UCSC.hg19)

Re: [Bioc-devel] VariantAnnotation::readVcf() sets the wrong seqlevelsStyle in devel

  seqlevels(vcf)   # [1] "chr22" or specify it later:   genome(vcf) <- "hg19"   seqinfo(vcf)   # Seqinfo object with 1 sequence from hg19 genome; no seqlengths:   #   seqnames seqlengths isCircular genome   #   chr22    NA NA   hg19 Hope this helps, H.

[Bioc-devel] VariantAnnotation::readVcf() sets the wrong seqlevelsStyle in devel

hi, it looks like either VariantAnnotation::readVcf() or something in the CollapsedVCF class broke in devel with respect to reading and setting sequence styles: library(VariantAnnotation) fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") vcf <- readVcf(fl, "hg19")

Re: [Bioc-devel] proposal for additional seqlevelsStyle

    QUAL  FILTER        rs1331956057  T  .    rs1252351580  G  .    rs1238523913  C  .    ---    seqinfo: 1 sequence from GRCh38 genome; no seqlengths On Fri, Dec 13, 2019 at 11:01 AM Robert Castelo wrote: h

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

y the build system during the INSTALL stage. How do people feel about that? H. > > Usually there is a single package that has changed and causes problems, and like in the present case a little detective work (once one knows what to look for) leads quic

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

Vince, thanks for the suggestions, i've taken the serializing route and submitted the fix. cheers, robert. On 05/06/2020 17:28, Vincent Carey wrote: > > > On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo <mailto:robert.cast...@upf.edu>> wrote: > > hi Vince, >

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

s4596632" "rs12203592" [11] "rs16891982" "rs1393350"  "rs1847134" thanks! robert. On 05/06/2020 14:06, Vincent Carey wrote: > I am really sorry about the situation with gwascat and will try to > straighten it out today. > > On Fri, Jun 5,

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

On 6/5/20, 7:58 AM, "Robert Castelo" wrote: never thought about it this way, but how can the system install something that does not build? how should *i* install something that does not build to reproduce the error? sorry if these are very naive questions!! ro

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

:27 AM, "Bioc-devel on behalf of Robert Castelo" wrote: hi, my package GenomicScores is not building, see: http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html apparently, it is breaking in the following lines of it

[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

hi, my package GenomicScores is not building, see: http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html apparently, it is breaking in the following lines of its vignette: library(gwascat) data(ebicat37) which in the report from the bioc build machine

Re: [Bioc-devel] Reducing dependencies

hi Koen, you can do some analysis of the dependencies using the BiocPkgTools as follows: library(BiocPkgTools) depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"), dependencies=c("Depends", "Imports")) ## if you get this error ## ## Error in readRDS(gzcon(con)) : ##   cannot open

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

em. Probably also worth mentioning the itdepends package ( https://github.com/r-lib/itdepends), which I think tries primarily to determine the relationship between package dependencies and lines of code, which seems like complementary information. Martin On 2/6/20, 12:29 PM, "Robert Castelo&

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

:sp.between(g, start="DT", finish="Matrix", detail=TRUE)[[1]]$path_detail [1] "DT""crosstalk" "ggplot2" "mgcv" "Matrix" ?? Martin On 2/6/20, 10:47 AM, "Robert Castelo" wrote: hi Martin,

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

leave the clever recursive or graph-based algorithm up to you, to report back to the mailing list? For what it's worth I think the last time this came up Martin Maechler pointed to a function in base R (probably the tools package) that implements this, too...? Martin Morgan O

[Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

hi, when i load the package 'GenomicScores' in a clean session i see thorugh the 'sessionInfo()' that the package 'Matrix' is listed under "loaded via a namespace (and not attached)". i'd like to know what is the dependency that 'GenomicsScores' has that ends up requiring the package

Re: [Bioc-devel] proposal for additional seqlevelsStyle

g and some significant refactoring. It wouldn't be just a matter of adding a column to genomeStyles()$Homo_sapiens. H. On 12/10/19 14:19, Robert Castelo wrote: I second this, and would suggest to name the style as 'GRC' for "Genome Reference Consortium". thanks Vince for bringing

Re: [Bioc-devel] proposal for additional seqlevelsStyle

I second this, and would suggest to name the style as 'GRC' for "Genome Reference Consortium". thanks Vince for bringing this up, being able to easily switch between genome styles is great. if 'paste0()' in R is one of the most influential contributions to statistical computing

Re: [Bioc-devel] progress with BiocParallel::bpiterate

of the iteration is known... is bpiterate() providing functionality (REDUCE, maybe? that bplapply() does not? Martin On 11/27/19, 1:11 PM, "Bioc-devel on behalf of Robert Castelo" wrote: hi, the 'BiocParallel::bpiterate()' method shows progress through the foll

[Bioc-devel] progress with BiocParallel::bpiterate

hi, the 'BiocParallel::bpiterate()' method shows progress through the following call: setMethod("bpiterate", c("ANY", "ANY", "SerialParam"),     function(ITER, FUN, ..., REDUCE, init, reduce.in.order = FALSE,     BPPARAM=bpparam()) { [...]     progress <-

Re: [Bioc-devel] Dependency to PEER

hi, it seems that the PEER repository hasn't been updated in the last 7 years and that the package is distributed under a GPL-2 license. if i'm interpreting this correctly, you could copy that code into your package redistributing it under the GPL-2 license and asking the users of PEER to

Re: [Bioc-devel] limma Suggests:statmod vs Imports:statmod

of limma that never use duplicateCorrelation or other functions that require statmod will never need to install it. For more info, see this old post about the same problem: https://support.bioconductor.org/p/16932/ Regards, Ryan On Thu, May 10, 2018 at 11:58 PM Robert Castelo <

[Bioc-devel] limma Suggests:statmod vs Imports:statmod

hi, this is a question for limma developers. at every new fresh installation of BioC and limma i get this message when i use 'duplicateCorrelation()': "statmod package required but is not installed" i just install 'statmod' and problem solved. this, however, triggers questions from some of

Re: [Bioc-devel] RareVariantVis failed

nges, ...) :   assuming query ranges genome build is the one of the GScores object (Genome Reference Consortium GRCh37). Error in match.names(clabs, nmi) : names do not match previous names Calls: chromosomeVis ... eval -> eval -> eval -> rbind -> rbind -> match.names I will be than

[Bioc-devel] VariantAnnotation: streaming over a genomic range

hi, when i use the function 'readVcf()' from the 'VariantAnnotation' package through a 'TabixFile' object, i can stream over it even if i do not specify the argument 'yieldSize', although in that case the streaming is trivial because is reading the whole file into main memory: CEUvcf <-

Re: [Bioc-devel] Warnings in build for BioCor

Lluis, something you can do in you NAMESPACE to follow the advice below from Matthias if you are importing the functionality of a whole package is: import(pkgyouneed, except=functionmethodyoudefine) in this way, you're importing everything except that particular function or method that you

Re: [Bioc-devel] gwaswloc class broken

  traveling but will tackle asap    if u can coerce to granges it may help as the only purpose of gwaswloc is to have a concise show method    but the coercion might fail too On Tue, Feb 20, 2018 at 6:43 AM Robert Castelo <robert.cast...@upf.edu <mailto:robert.cast...@upf.edu>> w

[Bioc-devel] gwaswloc class broken

hi, the 'gwasloc' class from the gwascat package seems to be broken in devel, i suspect due to recent changes in the 'GRanges' class or some other class upstream, because the definition of the 'gwasloc' class in gwascat/R/classes.R is: setClass("gwaswloc",

Re: [Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

(in version 1.15.18) so now you should be able to install it again. Sorry for the inconvenience, H. On 12/19/2017 12:31 AM, Robert Castelo wrote: hi, multiple packages, among them, Gviz or VariantFiltering, currently break in the build machines with the following error: Error : object

[Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

hi, multiple packages, among them, Gviz or VariantFiltering, currently break in the build machines with the following error: Error : object ‘path’ is not exported by 'namespace:Rsamtools' see, for instance:

Re: [Bioc-devel] S4Vectors::DataFrame, S4Vectors::cbind() and non-elementwise metadata

on Annotated derivatives (e.g. shift()) propagate the object-wise metadata, even though it's not clear that this information will still be relevant for the transformed object. Cheers, H. On 10/25/2017 07:39 AM, Robert Castelo wrote: hi, i've the following question on how 'S4Vectors::cbind

[Bioc-devel] S4Vectors::DataFrame, S4Vectors::cbind() and non-elementwise metadata

hi, i've the following question on how 'S4Vectors::cbind()' works on 'DataFrame' objects. let's say i have the following two toy 'DataFrame' objects, each of them including some elementwise and non-elementwise metadata (i hope i'm using the right terminology!): library(S4Vectors) dtf1 <-

Re: [Bioc-devel] GenomicRanges::cbind() problem

12, 2017 at 12:06 AM, Robert Castelo <robert.cast...@upf.edu> wrote: dear GenomicRanges developers, my package qpgraph is breaking in devel due to the following behavior of GenomicRanges: library(GenomicRanges) gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))

[Bioc-devel] GenomicRanges::cbind() problem

base other attached packages: [1] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 IRanges_2.10.3 [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 XVector_0.16.0 [4] GenomeInfoDbData_0.99.0 RCurl_1.95-4.8

[Bioc-devel] how to verify upstream git changes

hi, i've had a smooth transition from SVN to git for all the software packages i maintain (thanks for the great documentation!!) and i have the following question. i keep a local git repository for each of my software packages, hanging from my github account and this means that i have to

Re: [Bioc-devel] strand<- method for 'GPos' doesn't work

now if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method

Re: [Bioc-devel] strand<- method for 'GPos' doesn't work

great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: Hi Robert, I'm working on this. Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote: hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1

[Bioc-devel] strand<- method for 'GPos' doesn't work

hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1) <- "-" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GPos" traceback() 10: methods::slot(object, name) 9: getElement(x,

Re: [Bioc-devel] how to minimally serialize a FilterRules object

On 05/07/2017 20:39, Martin Morgan wrote: On 07/05/2017 12:59 PM, Robert Castelo wrote: dear developers, in the framework of a package i maintain, VariantFiltering, i'm using the 'FilterRules' class defined in the S4Vector package and i'm interested in serializing (e.g., saving to disk via

[Bioc-devel] how to minimally serialize a FilterRules object

dear developers, in the framework of a package i maintain, VariantFiltering, i'm using the 'FilterRules' class defined in the S4Vector package and i'm interested in serializing (e.g., saving to disk via 'saveRDS()') 'FilterRules' objects where some rules may defined using functions. my

Re: [Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

BiocInstaller_1.25.3 [22] GenomicFeatures_1.27.14 XML_3.98-1.5 On Wed, Apr 19, 2017 at 7:06 AM, Robert Castelo <robert.cast...@upf.edu> wrote: hi, it seems that recent changes to S4Vectors are breaking the coercion from the '*VCF' class to the 'VRanges' class. the traceback points to the private fu

[Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

hi, it seems that recent changes to S4Vectors are breaking the coercion from the '*VCF' class to the 'VRanges' class. the traceback points to the private function 'recycleVector() from the 'S4Vectors' package, please find below the minimal example that reproduces the problem with the session

Re: [Bioc-devel] build on different version

/checkResults/devel/bioc-LATEST/ For now I would not worry about the error on toluca2. Valerie On 04/14/2017 02:42 AM, Robert Castelo wrote: hi, on tuesday april 11th i checked in changes for VariantFiltering version 1.11.10 and i've seen that today the build for tuesday gives errors on version

[Bioc-devel] build on different version

hi, on tuesday april 11th i checked in changes for VariantFiltering version 1.11.10 and i've seen that today the build for tuesday gives errors on version 1.11.9 with snapshot date from april 7th. i do my devel changes in the github repo rcastelo/VariantFiltering and check them into SVN,

Re: [Bioc-devel] TabixFileList() constructor broken in devel

ist function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize = NA_integer_) { index <- as.character(index) .RsamtoolsFileList(file, index, ..., yieldSize = yieldSize, class = "TabixFile") } On Thu, Dec 29, 2016 at 11:5

Re: [Bioc-devel] TabixFileList() constructor broken in devel

tistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > -------- > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Robert Castelo <robert.cast...@upf.edu> &

[Bioc-devel] TabixFileList() constructor broken in devel

hi, the 'TabixFileList()' constructor in Rsamtools seems to be broken in devel: library(Rsamtools) example(TabixFileList) ## which actually does not construct any 'TabixFileList' TabixFileList(tbx) Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type

[Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

hi, there's a warning issued by GenomeInfoDb::keepStandardChromosomes() because of multiple compatible sequence styles, that i guess it should be corrected. this warning can be reproduced minimally as follows; library(GenomicRanges) library(GenomeInfoDb) gr <- GRanges(seqnames="1",

Re: [Bioc-devel] poor performance of snpsByOverlaps()

9"))) ) user system elapsed 0.237 0.055 16.476 faster than a speeding snplocs? but perhaps there is information loss or other diminished functionality On Fri, Jun 17, 2016 at 12:53 PM, Robert Castelo <robert.cast...@upf.edu <mailto:robert.cast...@upf.edu>> wrote:

[Bioc-devel] vignette metadata dissapeared in Sweave/PDF vignettes

hi, I have noticed that in the recent release of BioC the vignettes produced as Sweave/PDF documents do not show anymore the metadata written using %\VignetteIndexEntry{}, while this seems to work fine with the HTML vignettes. compare for instance the vignette metadata in the landing pages

Re: [Bioc-devel] Support site unavailable

immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health

Re: [Bioc-devel] Classes to be supported by ggraph

hi, i use the part of the functionality of the graph package within my packages qpgraph and VariantFiltering. I mostly use the 'graphBAM' class that provides a memory-efficient representation of the graph and the possiblity to store data associated with nodes and edges via the 'nodeData()'

Re: [Bioc-devel] seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles

, it sounds like the user should be able to do seqlevelsStyle(x) <- "Ensembl" independently of whether this will result in seqlevels that are the same as if s/he had done seqlevelsStyle(x) <- "NCBI". Cheers, H. On 01/25/2016 02:39 AM, Robert Castelo wrote: hi, i would l

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

ranscripts mapped to Entrez Gene IDs. I'll work on this and will also investigate makeTxDbFromGRanges's failure on AnnotationHub's GFF files from GENCODE. H. On 01/11/2016 06:29 AM, Robert Castelo wrote: hi, if i'm interpreting this correctly, the news archive of the UCSC

[Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

hi, if i'm interpreting this correctly, the news archive of the UCSC Genome Browser accessible here: http://genome.ucsc.edu/goldenPath/newsarch.html announced on June 29th, 2015, that they are discontinuing the generation of UCSC Known Genes annotations for human, and provide the Gencode

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

hi, On 01/11/2016 04:07 PM, Vincent Carey wrote: [...] Is it true that there is an asymmetry between Entrez gene ID and Ensembl gene ID for querying org.Hs.eg.db (I tend to prefer Homo.sapiens as a symbol mapping resource)? Both ENTREZID and ENSEMBL are listed as keytypes. My question is

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

bring these methods back if there is a way to preserve the semantic of base::ifelse() (which relies on delayed evaluation of the 'yes' and 'no' arguments). H. The goal with Rle was to make it behave as conveniently

[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

hi, one of the recent changes in the devel IRanges has been to defunct the 'ifelse' method for 'Rle' objects. This was warned during the previous devel cycle and so it does with current release. One of the affected functions is the VRanges object constructor, 'VRanges()'. Since I use this

Re: [Bioc-devel] upgrading

Try in a fresh run: remove.packages("BiocInstaller") source("http://bioconductor.org/biocLite.R;) cheers, robert. Original message From: Kasper Daniel Hansen Date:20/10/2015 16:55 (GMT+01:00) To: bioc-devel@r-project.org Subject:

Re: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

rote: Hi Robert, Thanks for reporting the bug. The problem was with how 'X' was split before dispatching to bplapply() and affected both SerialParam and SnowParam. Now fixed in release (1.2.21) and devel (1.3.52). Valerie - Forwarded Message - From: "Robert Castelo"<robert.cast...@up

Re: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

). Valerie - Forwarded Message - From: "Robert Castelo" <robert.cast...@upf.edu> To: bioc-devel@r-project.org Sent: Wednesday, September 2, 2015 8:12:33 AM Subject: [Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem hi, I have encountered a problem when

[Bioc-devel] BiocParallel::bpvec() and DNAStringSet objects, problem

hi, I have encountered a problem when using the bpvec() function from the BiocParallel package with DNAStringSet objects and the "SerialParam" backend: library(Biostrings) library(BiocParallel) ## all correct when using the multicore backend bpvec(X=DNAStringSet(c("AC", "GT")),

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

-- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550 ___ Bioc-devel@r

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

strand for at least 2 reasons: (1) to be less error prone [of course this runs completely counter to flexibility] and (2) simplicity [we don't have to worry about what - means for ref/alt, overlap, etc]. On Thu, Jun 11, 2015 at 6:05 AM, Robert Castelo robert.cast...@upf.edu wrote: one option for me

Re: [Bioc-devel] strandless introns with VariantAnnotation::locateVariants()

and strand is set to '*' if different strands are found in the same list element. The fix has been checked into release and devel. Valerie On 06/11/2015 03:26 AM, Robert Castelo wrote: hi Valerie, thanks for the fix, it seems that it required a more complex update than i initially thought looking

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

() output with its input. The one for VRanges might do something like the above. Michael On Thu, Jun 11, 2015 at 9:14 AM, Robert Castelo robert.cast...@upf.edu wrote: Of course, the inclusion of strand would imply an interpretation of the variant and its strand (e.g., -) with respect

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

/2015 09:49 PM, Michael Lawrence wrote: This changed recently. VariantAnnotation in devel no longer enforces a strand on VRanges, or at least it allows the * case. On Fri, May 22, 2015 at 11:33 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: Hi, I have

Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

for negative strand variants? On Wed, Jun 10, 2015 at 5:54 AM, Robert Castelo robert.cast...@upf.edu wrote: Michael, regarding our email exchange three weeks ago, I found a couple of places in VariantAnnotation that IMO need to be updated to avoid enforcing strand on VRanges. these places occur when

Re: [Bioc-devel] GSEABase::getOBOCollection() missing children

hi Martin, thanks for the quick fix!!! best regards, robert. On 06/05/2015 08:05 PM, Martin Morgan wrote: On 06/05/2015 08:51 AM, Robert Castelo wrote: hi, importing an OBO file with GSEABase::getOBOCollection() I have observed missing children in the imported ontology. Here is an example

[Bioc-devel] GSEABase::getOBOCollection() missing children

hi, importing an OBO file with GSEABase::getOBOCollection() I have observed missing children in the imported ontology. Here is an example with the Sequence Ontology: library(GSEABase) oboSOXP - getOBOCollection(http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo;) Warning message:

[Bioc-devel] MafDb.ExAC.r0.3.sites missing from build

hi, i have just noticed that VariantFiltering breaks in the last build: http://www.bioconductor.org/checkResults/3.1/bioc-LATEST/VariantFiltering/zin2-buildsrc.html and the reason is that the devel annotation package

Re: [Bioc-devel] MafDb.ExAC.r0.3.sites missing from build

oops, how embarrassing :*} thanks Dan, just did it. On 4/10/15 11:35 PM, Dan Tenenbaum wrote: Robert, you just need to put MafDb.ExAC.r0.3.sites in Depends, Suggests, or Imports. Dan - Original Message - From: Robert Castelo robert.cast...@upf.edu To: bioc-devel@r-project.org Sent

[Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

in my message below, the line that it says: head(loc_all$CDSID) it should say head(coding2$CDSID) cheers, robert. == hi, there is a little tiny bug in the current devel version of VariantAnnotation::predictCoding(), and more concretely within

Re: [Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

) To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] little tiny bug in CDSID annotations from predictCoding() Hi Robert, Thanks for reporting the typo and bug. Now fixed in 1.13.41. Valerie On 03/17/2015 10:58 AM, Robert Castelo wrote: in my message below, the line that it says

[Bioc-devel] little tiny bug in CDSID annotations from predictCoding()

hi, there is a little tiny bug in the current devel version of VariantAnnotation::predictCoding(), and more concretely within VariantAnnotation:::.localCoordinates(), that precludes the correct annotation of the CDSID column: library(VariantAnnotation)

[Bioc-devel] zero-width ranges representing insertions

dear devel people, specially Val and Michael, Hervé has recently added an annotation package that includes non-SNVs variants from dbSNP, it is called: library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38) if you execute the corresponding example you'll see the kind of information stored in the

Re: [Bioc-devel] zero-width ranges representing insertions

, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: dear devel people, specially Val and Michael, Hervé has recently added an annotation package that includes non-SNVs variants from dbSNP, it is called: library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38) if you

Re: [Bioc-devel] Changes to the SummarizedExperiment Class

[[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona

Re: [Bioc-devel] show method for CompressedVRangesList-class

are in the accessing of the elements. But this seems like too much longer, so I will look into it. On Wed, Feb 25, 2015 at 8:12 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: my current reason to prefer

Re: [Bioc-devel] show method for CompressedVRangesList-class

On Tue, Feb 24, 2015 at 2:36 PM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: so, yes, but IMO rather than inheriting the show method from a GRangesList, i think that the show method for CompressedVRangesList objects should be inherited from a VRangesList

Re: [Bioc-devel] show method for CompressedVRangesList-class

Lawrence wrote: If you're storing data on a relatively small number of individuals (say, hundreds), you should use SimpleVRangesList, not CompressedVRangesList. On Wed, Feb 25, 2015 at 7:10 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: i see you point

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