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 <micha...@gene.com> 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 would be nice if restrictToSNV just assumed that alt(x) must be
> something with nchar() support (with special handling for any List), so
> that the 'character' vector of alt,VRanges would work immediately.
> Basically restrictToSNV should just be x[isSNV(x)]. Is there even a
> use-case for the restrictToSNV abstraction if we did that?
>
> Michael
>
>
>
> On Tue, Mar 18, 2014 at 10:36 AM, Valerie Obenchain <voben...@fhcrc.org>wrote:
>
>> Hi,
>>
>> I've added a restrictToSNV() function to VariantAnnotation (1.9.46). The
>> return value is a subset VCF object containing SNVs only. The function
>> operates on CollapsedVCF or ExapandedVCF and the alt(VCF) value must be
>> nucleotides (i.e., no structural variants).
>>
>> A variant is considered a SNV if the nucleotide sequences in both
>> ref(vcf) and alt(x) are of length 1. I have a question about how variants
>> with multiple 'ALT' values should be handled.
>>
>> Should we consider row 4 a SNV? One 'ALT' is length 1, the other is not.
>>
>> ALT <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C"))
>> REF <- DNAStringSet(c("G", c("AA"), "T", "G"))
>>
>>> DataFrame(REF, ALT)
>>>>
>>> DataFrame with 4 rows and 2 columns
>>> REF ALT
>>> <DNAStringSet> <DNAStringSetList>
>>> 1 G A
>>> 2 AA TT
>>> 3 T G,A
>>> 4 G TT,C
>>>
>>
>>
>> Thanks.
>> Valerie
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
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