multiAllelicFilt {AllelicImbalance} | R Documentation |
filter on multiallelic snps
multiAllelicFilt(x, ...) ## S4 method for signature 'ASEset' multiAllelicFilt( x, strand = "*", threshold.count.sample = 10, threshold.frequency = 0.1, filterOver = "eachSample" )
x |
|
... |
internal param |
strand |
strand to infer from |
threshold.count.sample |
least amount of counts to try to infer allele |
threshold.frequency |
least fraction to classify (see details) |
filterOver |
'eachSample' or 'allSamples' |
based on the allele counts for all four variants A, T, G and C and returns true if there is counts enough suggesting a third or more alleles. The sensitivity can be specified using 'threshold.count.sample' and 'threshold.frequency'.
Jesper R. Gadin, Lasse Folkersen
#load example data data(ASEset) a <- ASEset multiAllelicFilt(a)