mlgt (version 0.16)

callGenotypes.default: Default internal methods for callGenotypes

Description

This is the default method to call genotypes from a table of variant counts. Methods:-

`callGenotypes.default'

Three sequential steps for each marker/sample pair:

1. if the number of reads is less than minTotalReads the genotype is `tooFewReads'
2. if the difference between the sum of counts of the top two variants and the count of the third most variant, expressed as proportion of total, is less than minDiffToVarThree, OR the third most abundant variant accounts for more than maxPropVarThree (default=0.1) of the reads, then the genotype is `complexVars'
3. if the difference between the counts of top two variants, expressed as a proportion of the total, is greater than or equal to minPropDiffHomHetThreshold, then the genotype is HOMOZYGOTE. Otherwise it is HETEROZYGOTE.

Usage

callGenotypes.default(table, minTotalReads = 50, minDiffToVarThree = 0.4, minPropDiffHomHetThreshold = 0.3, maxPropVarThree = 0.1)

Arguments

table

The table of sequence counts as in the markerSampleTable of an mlgtResult object.

minTotalReads

Minimum number of reads before attempting to call genotypes

minDiffToVarThree

Difference between sum of counts of top two variants and the count of the third most frequent variant, expressed as proportion of total.

minPropDiffHomHetThreshold

Difference between counts of top two variants. One way to distinguish HOMOZYGOTES and HETEROZYGOTES.

maxPropVarThree

Also call as 'complexVars' if the third variant accounts for more than this proportion of used reads (default=0.1)

Value

A data.frame identical to those in markerSampleList but with additional columns giving parameter values, and a 'status' column giving the genotype status.