getGenotype-stringCoverageList-method: Assigns genotype.

In svilsen/STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data

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

## S4 method for signature 'stringCoverageList'
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)

svilsen/STRMPS documentation built on May 31, 2019, 7:55 a.m.