getGenotype {STRMPS}

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)

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.

Value

Returns a list, with an element for every marker in stringCoverageList-object, each element contains the genotype for a given marker.

Examples

# Strings aggregated by 'stringCoverage()'
data("stringCoverageList")

getGenotype(stringCoverageList)