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
<st...@channing.harvard.edu>wrote:
>
>
>
> On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence <
> lawrence.mich...@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?
>>
>>
> for VCF instance it would be x[isSNV(x),] and indeed I think that would be
> sufficient. i like the idea of having this family of predicates for
> variant classes to allow such selections
>
>
>
>> 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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