getGenotype: Assigns genotype.
Description
getGenotype takes an stringCoverageList-object, assumes the sample is a reference file and assings a genotype, based on a heterozygote threshold, for every marker in the provided list.
Usage
getGenotype(
stringCoverageListObject,
colBelief = "Coverage",
thresholdSignal = 0,
thresholdHeterozygosity = 0.35,
thresholdAbsoluteLowerLimit = 1
)
Value
Returns a list, with an element for every marker in stringCoverageList-object, each element contains the genotype for a given marker.
Arguments
- stringCoverageListObject
an stringCoverageList-object, created using the stringCoverage-function.
- colBelief
the name of the coloumn used for identification.
- thresholdSignal
threshold applied to the signal (generally the coverage) of every string.
- thresholdHeterozygosity
threshold used to determine whether a marker is hetero- or homozygous.
- thresholdAbsoluteLowerLimit
a lower limit on the coverage for it to be called as an allele.
Examples
Run this code# Strings aggregated by 'stringCoverage()'
data("stringCoverageList")
getGenotype(stringCoverageList)
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