Hi Robert, Michael,
On 10/24/2014 04:21 PM, Robert Castelo wrote:
you're right, i was just thinking about b37 (w/o MT) and hg19 but one
can have the same seqlevelsStyle with two different builds such as hg18
and hg19. Well then, the solution i was using below,
genome(vcf) <- genome(txdb)[inter
you're right, i was just thinking about b37 (w/o MT) and hg19 but one
can have the same seqlevelsStyle with two different builds such as hg18
and hg19. Well then, the solution i was using below,
genome(vcf) <- genome(txdb)[intersect(names(genome(vcf)),
names(genome(txdb)))]
was not that bad, b
Not sure I understand. Setting the seqlevelsStyle cannot change the genome
build, so the two Seqinfos will remain incompatible in that way. I think
what you want is to be able to say "let's consider these two genome builds
to be the same", which seems reasonable after dropping chrM. I was
proposing
hi Michael,
if we assume that a seqname style does not imply a specific genome
build, then i'd say that the error below about having incompatible
genomes should not pop up because sequence styles have been already
matched, right?
On 10/24/14 10:22 PM, Michael Lawrence wrote:
> I don't think a
Just an update, we have updated the vignette "Submitting your Organism
to GenomeInfoDb" with contact information.
Please send all subsequent "organism" requests to
"maintai...@bioconductor.org"
Thanks,
Sonali
On 10/22/2014 9:10 AM, Sonali Arora wrote:
Hi Leo,
You can contact me for adding a
I don't think a seqname style implies a specific genome build. But the
inverse might make sense. Given a genome build identifier, we could check
for consistent naming. Perhaps an option on "genome<-" could support this?
On Fri, Oct 24, 2014 at 11:52 AM, Valerie Obenchain
wrote:
> This is a goo
Hi Leo,
This bug is now fixed .
JGI2 was being incorrectly returned previously.
The correct style is JGI2.F and from now on, it will always check only
for JGI2.F
> library(GenomeInfoDb)
> seqlevelsStyle("T")
[1] "JGI2.F"
> seqlevelsStyle("LGI")
[1] "NCBI"
> mapSeqlevels('LGI', 'JGI2.F')
[1] "T
This is a good question. I'm not sure we want seqlevelsStyle() to also
alter the genome value. I think it's a reasonable request but I'd like
to open it up to discussion. I've cc'd a few others for input.
Valerie
On 10/24/14 09:05, Robert Castelo wrote:
hi Valerie,
thanks for the quick fix
hi Valerie,
thanks for the quick fix and updating the documentation, i have a
further question about the seqinfo slot and particularly the use of
seqlevelsStyle(). Let me illustrate it with an example again:
==
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
