[Bioc-devel] [VariantAnnotation]

[Valerie Obenchain]

Correction below.


On 11/20/2013 09:59 AM, Valerie Obenchain wrote:
> Hi Delphine,
>
> I've cc'd your message to the Bioconductor mailing list. We have two
> lists, one for general questions and the other for bug reports/feature
> requests. Please post future questions to one of these lists instead of
> sending them to a single person. The lists reach a wider audience and
> others can chime in with their responses/experience. You can find info
> about the mailing lists here,
>
> http://www.bioconductor.org/help/mailing-list/
>
> If you would like to submit a patch for 'fixed<-' on a VCFHeader I'd be
> happy to take a look at it. This replacement method was not added along
> with the others because changes made to 'fixed' must be compatible with
> writeVcf() and expand(). The most important components of this are
> appropriate elementLengths of REF and ALT. The replacement method should
> have validity checks for VCFHeader and confirmation that writeVcf()
> outputs a valid vcf and expand() can unlist the data.

Sorry, expand() is not relevant here - I was thinking of data 
replacement not header. The header is a much simpler case. This 
shouldn't be to bad. I'll put it on the TODO.

Valerie


>
> Thanks.
> Valerie
>
>
> On 11/15/2013 05:39 AM, delphine charif wrote:
>> Hi Valerie,
>>
>> Thank you very much. I installed the devel branch of VariantAnnotation
>> and used the 'geno<-' replacement method
>> for VCFHeader and everything goes well.
>> But ... :-) ... now, tried to use 'fixed<-' as a replacement method
>> (Would like to added filters to the original VCF) for
>> VCFHeader and got this message:
>>
>> Erreur dans (function (classes, fdef, mtable) :
>> unable to find an inherited method for function ‘fixed<-’ for signature
>> ‘"VCFHeader", "SimpleDataFrameList"’
>>
>> Do you think that you will also implement this replacement method ?
>>
>> Thank you very much for your reactivity.
>>
>> Best regards.
>>
>> Delphine.
>>
>> Le 05/11/13 01:44, Valerie Obenchain a écrit :
>>> Hi Delphine,
>>>
>>> In 1.9.5 (devel branch) I've added 'meta<-', 'info<-' and 'geno<-'
>>> replacement methods for VCFHeader.
>>>
>>> fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
>>> vcf <- readVcf(fl, "hg19")
>>>
>>> newInfo <- DataFrame(Number=1, Type="Integer",
>>> Description="Number of Samples With Data",
>>> row.names="NS")
>>> info(header(vcf)) <- rbind(info(hdr), newInfo)
>>>
>>>
>>> There is also a 'header<-' method that replaces the entire VCFHeader
>>> in a VCF object.
>>>
>>> hdr <- header(vcf)
>>> meta(hdr)[3,1] <- "myNewSource"
>>> header(vcf) <- hdr
>>>
>>> Let me know if you run into problems.
>>>
>>> Valerie
>>>
>>>
>>> On 10/15/2013 07:48 AM, delphine charif wrote:
>>>> Dear Valerie,
>>>>
>>>> Thank you very much for your work on the package VariantAnnotation.
>>>> We are using this package
>>>> and we would like to know if there is a way to update the VCFheader of
>>>> an existing VCF object.
>>>>
>>>> By example:
>>>>
>>>> genodf <- DataFrame(
>>>> Number=rep("1",2),
>>>> Type=c("String","String"),
>>>> Description=c("Genotype", "Genotype Likelihoods")
>>>> )
>>>> row.names(genodf)=c("GT","GL")
>>>>
>>>> We would like to do something like:
>>>>
>>>> geno(header(VCFobject)) <- genodf
>>>>
>>>>
>>>> Thank you very much in advance.
>>>>
>>>> Best regards.
>>>>
>>>>
>>>
>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel