Related to this:
I have added getters for seqinfo (and friends) for the OrganismDb
objects. I have not added the setters yet though since that requires
some refactoring of what an OrganismDb object actually is internally.
But I intend to do this also.
Marc
On 04/25/2013 09:32 AM, Valerie Obenchain wrote:
Hi Vince, Kasper,
cc'ing Herve and Marc.
I think we have a couple of things going on so I wanted to clarify.
The 'genome' argument to readVcf() is assigned to the GRanges in
rowData with the "genome<-" setter. This is where .normargGenome()
gets called.
setReplaceMethod("genome", "Seqinfo",
function(x, value)
{
x@genome <- .normargGenome(value, seqnames(x))
x
}
)
If the 'genome' replacement value is named, the name(s) must match the
seqnames, not the build. So we aren't talking about matching
compatible builds,
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, c("b37"="hg19")) ## this is wrong
vcf <- readVcf(fl, c("hg19"="hg19")) ## also wrong
Instead the name must be the seqname, the value is the build,
vcf <- readVcf(fl, c("20"="hg19")) ## correct
vcf <- readVcf(fl, "hg19") ## also correct
This requirement for 'genome' is not well documented on ?readVcf or
?Seqinfo. We can fix that.
The second thing is the issue of a flexible mapping between seqinfo
metadata for different institutions. Herve and Marc have worked on
this in AnnotationDbi. They can explain more about the 'SeqnameStyle'
and how it might be used more widely.
Val
On 04/25/2013 06:54 AM, Kasper Daniel Hansen wrote:
An "official" comment on this
http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19
with some more info in this discussion
https://groups.google.com/a/soe.ucsc.edu/forum/?fromgroups=#!topic/genome/hFp-dGG9gBs
Essentially it seems the b37 has been "patched" and this patched
release is
not reflected in hg19 but may be (I don't know) reflected in the b37
download from NCBI
Kasper
On Thu, Apr 25, 2013 at 9:49 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
I agree with Vincent. I have seen code from Herve in a package with
some
standardization of chromosome names, and this code could perhaps be
used
more widely so we don't have all the problems with chr1 vs chr01 vs 1.
However, in this particular case, if Ulrich is actually interested
in the
mitochondrial genome, he has a problem.
hg19, which is the genome version from UCSC is consider equal to NCBIs
b37. However, as far as I understand, UCSC screwed up with the
mitochondrial genome and used an old version for their hg19. So the
error
message is in many ways right here: the two genomes are slightly
different
because they have different mitochondrial genomes.
Kasper
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