Question: (Closed) filter based on variant annotation
0
gravatar for winstondunnmd
12 weeks ago by
winstondunnmd0 wrote:

Dear Bioconductors:

I am doing SKAT test of genes based on their position on the chromosome. I use the following TopmedPipeline function and codes. I hope to additionally filter based on variant annotation. I have identified missense_variants and recorded their variant.id in a vector. Is it possible to additionally filter based on a vector that contains variant.id of the missense_variants?

Many thanks!

Winston

aggVarList <- aggregateGRanges(aggByPos)
seqResetFilter(seqData, verbose=FALSE)
iterator <- SeqVarRangeIterator(seqData, variantRanges=aggVarList, verbose=FALSE)
assoc <- assocTestAggregate(iterator, nullmod, test="SKAT", AF.max=0.1, weight.beta=c(1,25))
ADD COMMENTlink written 12 weeks ago by winstondunnmd0

Hello winstondunnmd!

We believe that this post does not fit the main topic of this site.

TopMedPipeline isn't a Bioconductor package. You could try biostars.org or stackoverflow.org

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 12 weeks ago by James W. MacDonald51k
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