On Thu, Dec 22, 2011 at 2:46 AM, Jane Merlevede <jane.merlevede@gmail.com>wrote:

> Thanks for your answer !
> I'm interesting in using the package that you developed:
> VariantAnnotation. I will try it after installing R.2.14
> At the beginning of your vignette, you show your data ; there is a column
> "strand". I would like to know if it cares about the strand, because that
> is why I need. I went through your paper and I haven't seen that you
> consider both direct and reverse strand. Does your package handle both
> strands? Or do I need to use the ReverseComplement function first and then
> use your method on only direct strand?
>
>
It uses the strand where sensible, I think. Like in predictCoding().
Valerie is the ultimate authority; it's really her package.

Michael


> Jane Merlevède
>
>
>
>
> 2011/12/20 Michael Lawrence <lawrence.michael@gene.com>
>
>> I think you are looking for the reverseComplement function in Biostrings.
>> Also, the VariantAnnotation package provides much of the functionality of
>> Annovar.
>>
>> Michael
>>
>> On Mon, Dec 19, 2011 at 2:13 AM, Jane Merlevede <jane.merlevede@gmail.com
>> > wrote:
>>
>>> Hello,
>>>
>>> I am looking for "interesting" mutations among a set of mutations. To
>>> reduce the amount of mutations, I am using Annovar. This software takes
>>> as
>>> input a file which contains the following information: chromosome, wild
>>> and
>>> mutated nucleotide(s) and the start and end position of the variant(s).
>>> It seems that this soft use only information from the "direct" sense but
>>> I
>>> have information on reverse strand too.
>>> I wrote a R-script to "reverse" the mutated variants, but I was told that
>>> there is probably a solution to do that in bioconductor.
>>> I haven't found yet, that's why I would like your help to know if it
>>> exists.
>>>
>>> Thanks in advance,
>>> Jane
>>>
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>>>
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>>
>>
>

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