OHperSNP {sequoia} | R Documentation |
Estimate Genotyping Error Rate
Description
Estimate genotyping error rate from Mendelian errors per SNP.
Usage
OHperSNP(GenoM, Par, Dups = NULL)
Arguments
GenoM |
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. |
Par |
pedigree dataframe, only genotyped parents are used. |
Dups |
pairs of duplicates |
Value
A dataframe with columns:
n.dam , n.sire , n.pair |
Number of dams, sires, parent-pairs successfully genotyped for the SNP |
OHdam , OHsire |
Count of number of opposing homozygous cases |
MEpair |
Count of Mendelian errors, includes opposing homozygous cases |
n.dups , n.diff |
Number of duplicate pairs successfully genotyped for the SNP; number of differences |
See Also
[Package sequoia version 2.11.2 Index]