#load example data
data(reads)
data(GRvariants)
#get counts at the three positions specified in GRvariants
alleleQualityArray <- getAlleleQuality(BamList=reads,GRvariants)
#place in ASEset object
alleleCountsArray <- getAlleleCounts(BamList=reads,GRvariants,
strand='*', return.class="array")
a <- ASEsetFromArrays(GRvariants, countsUnknown = alleleCountsArray)
aquals(a) <- alleleQualityArray
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