R: Plot genotyping evidence

plotGenotypeEvidence {mlgt} | R Documentation

## 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.

### 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

### Value

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

### 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)

[Package mlgt version 0.16 Index]