genotype matrix, in sequoia's format: 1 column per SNP, 1 row per individual, genotypes coded as 0/1/2/-9, and rownames giving individual IDs.

pedigree dataframe, only genotyped parents are used.

function that takes the genotyping error rate Err as input, and returns a 3x3 matrix of observed (columns) conditional on actual (rows) genotypes, or choose from inbuilt ones as used in sequoia 'version2.0', 'version1.3', or 'version1.1'. See ErrToM.

Error rate, as estimated from the joined offspring-parent (-parent) genotypes and the presumed error structure (ErrFlavour)

Number of dams, sires, parent-pairs succesfully genotyped for the SNP

Count of number of opposing homozygous cases

Count of Mendelian errors, includes opposing homozygous cases