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
>
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