detectAI(x, ...)
"detectAI"(x, return.class = "DetectedAI", strand = "*", threshold.frequency = 0, threshold.count.sample = 1, threshold.delta.frequency = 0, threshold.pvalue = 0.05, inferGenotype = FALSE, random.ref = FALSE, function.test = "binom.test", verbose = TRUE, gc = FALSE, biasMatrix = FALSE)
return.type 'ref' return only AI when reference allele is more expressed. 'alt' return only AI when alternative allele is more expressed or 'all' for both 'ref' and 'alt' alleles. Reference allele is the one present in the reference genome on the forward strand.
threshold.delta.frequency and function.test will use the value in mapBias(x) as expected value.
function.test will use the two most expressed alleles for testing. Make therefore sure there are no tri-allelic SNPs or somatic mutations among the SNPs in the ASEset.
inferGenotype(), set TRUE it should be used with as much samples as possible. If you split up the samples and run detectAI() on each sample separately, please make sure you have inferred the genotypes in before hand, alternatively used the genotypes detected by another variantCaller or chip-genotypes. Use ONLY biallelic genotypes.
#load example data
data(ASEset)
a <- ASEset
dai <- detectAI(a)
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