listCodingErrors: Generate a list of encoding errors
In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description Usage Arguments Details Value

Generate a list of encoding errors from genetic data

1	listCodingErrors(founders, finals, hetData)

`founders`	Genetic data for the founding lines of the population
`finals`	Genetic data for the final lines of the population
`hetData`	Data about the encoding of marker heterozygotes

Given genetic data matrices for the founding lines and the final lines of a population, and information about the encoding of marker heterozygotes, generate a list of errors. These errors include observed values which don't correspond to a known combination of marker alleles, missing values in the genetic data for the founding lines, etc.

The results of this function allow human-readable lists of errors to be generated, or errors to be automatically fixed (if the errors are sufficiently simple).

List with the following entries:

finals: Markers with an invalid observed value.
null: Markers with a missing value for a founding line, for which the are observations for at least one genetic line.
missingHetData: Markers for which a homozygote did not have an encoding.
invalidHetData: Markers for which the heterozygote encoding data was invalid.