mlgt (version 0.16)

plotGenotypeEvidence: Plot genotyping evidence

Description

Plot the distributions of values used in calling genotypes.

Arguments

callList

A list of genotypes calls.

genotypeCall

A single table of genotype calls

file

The file to write to.

Value

Creates six plots for each marker with a genotypeCall table. See details.

Details

Currently only makes sense with "custom" method. The resulting plots are

1. Histogram of the number of sequences assigned to each sample
2. Histogram of diffToVarThree parameter. Used to decide whether to make the call
3. Histogram of propDiffHomHet parameter. Used to distinguish HOMOZYGOTES and HETEROZYGOTES
4. propDiffHomHet against diffToVarThree
5. diffToVarThree against number of sequences
6. propDiffHomHet against number of sequences

See Also

callGenotypes

Examples

## Not run: 
# data("mlgtResult", package="mlgt")
# my.genoytpes <- callGenotypes(my.mlgt.Result)
# plotGenotypeEvidence(genotypeCall=my.genotypes[["DPA1_E2"]])
# ## End(Not run)