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))