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 style if they are not.
The 3 tasks are orthogonal. I guess most of
On 06/05/2015 11:43 AM, Michael Lawrence wrote:
On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org 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
- Original Message -
From: Jennifer Tom tom.jenni...@gene.com
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: Jennifer Tom tom.jenni...@gene.com, 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
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
- Original Message -
From: Jennifer Tom tom.jenni...@gene.com
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
On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org 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
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
Hi Dan,
Thank you for your quick response! The package is genotypeeval,
Jen
On Fri, Jun 5, 2015 at 10:33 AM, Dan Tenenbaum dtene...@fredhutch.org
wrote:
- Original Message -
From: Jennifer Tom tom.jenni...@gene.com
To: bioc-devel@r-project.org
Sent: Friday, June 5, 2015
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 lawrence.mich...@gene.com
wrote:
On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org 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:
library(GSEABase)
oboSOXP -
getOBOCollection(http://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo;)
Warning message:
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
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
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. tim.tri...@gmail.com
wrote:
maybe standardizeSeqinfo or
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
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
maybe standardizeSeqinfo or fixSeqinfo is clearer after all
Statistics is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science
On Fri, Jun 5, 2015 at 1:41 PM, Gabe Becker becker.g...@gene.com wrote:
On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr.
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
On Fri, Jun 5, 2015 at 1:19 PM, Michael Lawrence lawrence.mich...@gene.com
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.
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
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 the
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,
how about just
gr - addSeqinfo(gr, hg19)
Statistics is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science
On Fri, Jun 5, 2015 at 1:36 PM, Hervé Pagès hpa...@fredhutch.org wrote:
On 06/05/2015 01:19 PM, Michael Lawrence wrote:
To support the multi-genome
On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. 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, hg19)
instead?
~G
--
Gabriel Becker, Ph.D
Computational
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 hcorr...@gmail.com wrote:
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