Update on these tasks.
1) XStringSetList now has an nchar() method (as of Biostrings 2.31.17)
2) restrictToSNV() was removed from VariantAnnotation
3) The following generics and methods for VCF and VRanges have been
added to VariantAnnotation 1.9.50:
isSNV()
isInsertion()
isDeletion()
isInde
Some of the inconsistency emerges from wrappers that correspond to
operations on the rowData. I think that's fine as long as it's obvious (as
in the case of findOverlaps and isSNV). The head and tail functions are by
convention row-based for rectangular objects. I agree though that if we
keep 1D e
Hi Martin,
On 03/21/2014 01:45 PM, Martin Morgan wrote:
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little
surprising;
I learned it from restrictToSNV.
This is inherited from Summariz
1D extraction on matrices (treating them as a 1D vector) is actually
useful, but I don't see how that would really make sense here. This is an
inconsistency, and inconsistencies are often OK when there is a benefit
(like gr$foo), but unless I'm missing something the benefit here seems to
be x[i] vs
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
This is inherited from SummarizedExperiment:
> example(SummarizedExperiment)
> se
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
[...]
Following that logic names(se1) also probably return colnames(se1).
/\
should
H.
H.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
wrote:
On Wed, Mar 19, 2014 at 4:00
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
This is inherited from SummarizedExperiment:
> example(SummarizedExperiment)
> se1
class: SummarizedExperiment
dim: 200 6
Thanks Sean. Probably also need an "isSubstitution" for any substitution,
either SNV or complex.
On Wed, Mar 19, 2014 at 3:20 PM, Sean Davis wrote:
>
>
> On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain wrote:
>
>> Thanks for the feedback.
>>
>> I'll look into nchar for XStringSetList.
>>
>>
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain wrote:
> Thanks for the feedback.
>
> I'll look into nchar for XStringSetList.
>
> I'm in favor of supporting isDeletion(), isInsertion(), isIndel() and
> isSNV() for the VCF classes and removing restrictToSNV(). I could add an
> argument 'all_alt
Thanks for the feedback.
I'll look into nchar for XStringSetList.
I'm in favor of supporting isDeletion(), isInsertion(), isIndel() and
isSNV() for the VCF classes and removing restrictToSNV(). I could add an
argument 'all_alt' or 'all_alt_agreement' to be used with CollapsedVCF
in the case w
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
wrote:
>
>
>
> On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence <
> lawrence.mich...@gene.com> wrote:
>
>> It would be nice to have funct
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence wrote:
> It would be nice to have functions like isSNV, isIndel, isDeletion, etc
> that at least provide precise definitions of the terminology. I've added
> these, but they're designed only for VRanges. Should work for ExpandedVCF.
>
> Also, it w
Also, the code for DNAStringSetList is too low-level. There should just be
an nchar,XStringSetList that does the same thing as
nchar,CompressedCharacterList. Then restrictToSNV or whatever just does
any(nchar(x) == 1L) for any List.
Michael
On Wed, Mar 19, 2014 at 1:00 PM, Michael Lawrence wrot
It would be nice to have functions like isSNV, isIndel, isDeletion, etc
that at least provide precise definitions of the terminology. I've added
these, but they're designed only for VRanges. Should work for ExpandedVCF.
Also, it would be nice if restrictToSNV just assumed that alt(x) must be
somet
I would say rows 1 and 3 are SNVs, but not row 4. For this application
I think a variant has to be an SNV or not, as you can't pass half a
variant. (I suppose you could remove the ALT values with length > 1 and
set those genotypes to missing, but that is both complicated and
unexpected behavi
Hi Valerie,
I would consider G>C an SNV, G>TT not. But I assume that there exists
no clear consensus on this. How about a flag that let's the second pass
as SNV optionally, so everybody can get what one needs?
Best wishes
Julian
On 18/03/14 18:36, Valerie Obenchain wrote:
> Hi,
>
> I've adde
16 matches
Mail list logo
