mlgt (version 0.16)

errorCorrect: Alignment error correction

Description

Correct very low frequency site variants.

Arguments

mlgtResultObject

An object of class mlgtResult

correctThreshold

The maximimum Minor Allele Frequency (MAF) at which variants will be corrected.

Value

A new mlgtResult object with errors 'corrected'

Details

You may want to alter some of the sequences if you believe that sequences at very low frequency (within the set of sequences from a marker/sample pair) represent sequencing errors. errorCorrect() is implemented as an additional step after running mlgt, however, it is recommended to include error correction within mlgt using the errorCorrect=TRUE option. Using alignReport beforehand may help you decide whether to do this.

See Also

alignReport