Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

That's already possible, basically: seqinfo(gr) <- seqinfo(Mus.musculus) Anyway, I'm with Tim's last suggestion. Just support both. Have an argument to genome<- like standardize=FALSE for low-level manipulation. On Fri, Jun 5, 2015 at 1:56 PM, Hector Corrada Bravo wrote: > Sorry if I'm too lat

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Sorry if I'm too late for this... I think having "hg19" in 'gr <- standardizeSeqinfo(gr, "hg19")' be responsible for so much, can make this new function hard to maintain. Might it be better if that argument takes an object corresponding to a canonical annotation? E.g., library(Mus.musculus) gr <

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

how about: foo <- paintBikeShed("mauve") ## :-D more serious-like, though, genome(gr) <- "hg19" ## and gr <- standardizeGenome(gr, "hg19") seem like the apotheosis of clarity and thus the way to go. Statistics is the grammar of science. Karl Pearson

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On 06/05/2015 01:48 PM, Gabe Becker wrote: I dunno, standardizeSeqInfo just seems really long for a function name users are going to have to call. At the risk of annoying Herve further, what about gr <- castSeqInfo(gr, "gh19") gr! ? ~G On Fri, Jun 5, 2015 at 1:46 PM, Tim Triche,

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

I dunno, standardizeSeqInfo just seems really long for a function name users are going to have to call. At the risk of annoying Herve further, what about gr <- castSeqInfo(gr, "gh19") ? ~G On Fri, Jun 5, 2015 at 1:46 PM, Tim Triche, Jr. wrote: > maybe standardizeSeqinfo or fixSeqinfo is clea

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

maybe standardizeSeqinfo or fixSeqinfo is clearer after all Statistics is the grammar of science. Karl Pearson On Fri, Jun 5, 2015 at 1:41 PM, Gabe Becker wrote: > > > On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. > wrote: > >> how about

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Not a big fan of the gets (<-) syntax for "verb" functions. standardizeSeqinfo() is probably the most "proper" name according to our nomenclature. But novice users are still just going to want to do genome(gr) <- "hg19" and have it just the right thing. On Fri, Jun 5, 2015 at 1:36 PM, Hervé Pagès

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On 06/05/2015 01:41 PM, Gabe Becker wrote: On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. mailto:tim.tri...@gmail.com>> wrote: how about just gr <- addSeqinfo(gr, "hg19") Add sounds like it's, well, adding rather than replacing (Which it sometimes would do. gr <- fixSeqInfo(gr, "h

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On 06/05/2015 01:39 PM, Tim Triche, Jr. wrote: how about just gr <- addSeqinfo(gr, "hg19") mmh, we don't really "add" a seqinfo. We transform the existing one. This transformation can be called "standardization", or "normalization", or... but I wouldn't call it "addition". H. Statistics is

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. wrote: > how about just > > gr <- addSeqinfo(gr, "hg19") > Add sounds like it's, well, adding rather than replacing (Which it sometimes would do. gr <- fixSeqInfo(gr, "hg19") instead? ~G -- Gabriel Becker, Ph.D Computational Biologist Genente

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

how about just gr <- addSeqinfo(gr, "hg19") Statistics is the grammar of science. Karl Pearson On Fri, Jun 5, 2015 at 1:36 PM, Hervé Pagès wrote: > On 06/05/2015 01:19 PM, Michael Lawrence wrote: > >> To support the multi-genome case, one c

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On 06/05/2015 01:19 PM, Michael Lawrence wrote: To support the multi-genome case, one could set the genome as a vector, one value for each seqname, and it would fix the style/seqlength per seqname. It could sort by the combination of seqname and species. Presumably it would do nothing for unknown

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On Fri, Jun 5, 2015 at 1:19 PM, Michael Lawrence wrote: > To support the multi-genome case, one could set the genome as a > vector, one value for each seqname, and it would fix the > style/seqlength per seqname. It could sort by the combination of > seqname and species. Presumably it would do not

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

To support the multi-genome case, one could set the genome as a vector, one value for each seqname, and it would fix the style/seqlength per seqname. It could sort by the combination of seqname and species. Presumably it would do nothing for unknown genomes. But I agree that a standardizeSeqinfo()

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Hi Gabe, I wouldn't say "wrong" but "not normalized". So maybe for example everything is ok with their seqinfo but the seqlevels are not in canonical order, and, for whatever reason, they want to keep them that way (the actual order of the seqlevels impacts the sorting of the ranges in the GRange

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

That sounds like it calls for an (class-style) inheritence/genome-union model to me. I should probably stop talking now before the people who would have to implement that start throwing things at me, though. ~G On Fri, Jun 5, 2015 at 12:54 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com>

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

In WGBS we frequently sequence a human with spikein from the lambda genome. In this case, most of the chromosomes of the Granges are from human, except one. This is a usecase where genome(GR) is not constant. I suggest, partly for compatibility, to keep genome, but perhaps do something like st

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Herve, This is probably a naive question, but what usecases are there for creating an object with the wrong seqinfo for its genome? ~G On Fri, Jun 5, 2015 at 11:43 AM, Michael Lawrence wrote: > On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès wrote: > > I also think that we're heading towards som

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On 06/05/2015 11:43 AM, Michael Lawrence wrote: On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès wrote: I also think that we're heading towards something like that. So genome(gr) <- "hg19" would: (a) Add any missing information to the seqinfo. (b) Sort the seqlevels in "canonical" order.

Re: [Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès wrote: > I also think that we're heading towards something like that. > > So genome(gr) <- "hg19" would: > > (a) Add any missing information to the seqinfo. > (b) Sort the seqlevels in "canonical" order. > (c) Change the seqlevels style to UCSC st

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

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 with the Sequence Ontology: Thanks Robert, the import went ok, but the coercion to graphNEL was flawed. This

Re: [Bioc-devel] new error when submitting package 'there is no package called 'codetoolsBioC''

Hi Dan, Thank you for your quick response! The package is genotypeeval, Jen On Fri, Jun 5, 2015 at 10:33 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Jennifer Tom" > > To: bioc-devel@r-project.org > > Sent: Friday, June 5, 2015 10:30:39 AM > > Subject: [Bioc-devel]

Re: [Bioc-devel] new error when submitting package 'there is no package called 'codetoolsBioC''

- Original Message - > From: "Jennifer Tom" > To: "Dan Tenenbaum" > Cc: "Jennifer Tom" , bioc-devel@r-project.org > Sent: Friday, June 5, 2015 10:41:16 AM > Subject: Re: [Bioc-devel] new error when submitting package 'there is no > package called 'codetoolsBioC'' > > > Hi Dan, > >

Re: [Bioc-devel] new error when submitting package 'there is no package called 'codetoolsBioC''

- Original Message - > From: "Jennifer Tom" > To: bioc-devel@r-project.org > Sent: Friday, June 5, 2015 10:30:39 AM > Subject: [Bioc-devel] new error when submitting package 'there is no package > called 'codetoolsBioC'' > > I made minor changes to my package and resubmitted it to > B

[Bioc-devel] new error when submitting package 'there is no package called 'codetoolsBioC''

I made minor changes to my package and resubmitted it to Bioconductor. It previously checked without errors. I now get an error message: Failed with error: 'there is no package called 'codetoolsBioC'' and am uncertain how to address this. Any insight appreciated. Thanks! Jen [[alte

[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 messag

Re: [Bioc-devel] Changes in AnnotationDbi

I agree that a warning is probably not the way to go, as it does imply that there might have been something wrong with either the input or output. Plus, not everybody understands the distinction between error and warning. And having additional documentation can't possibly hurt. But that assumes th

Re: [Bioc-devel] reproducible with mclapply?

On Thu, 04-06-2015, at 15:50, Kasper Daniel Hansen wrote: > Note you're not guaranteed that two random streams starting with different > seeds will be (approximately) independent, so the suggestion on SO makes > the numbers reproducible but technically wrong. > But whether or not that is a pr