EstEr: Estimate genotyping error rate

In sequoia: Pedigree Inference from SNPs

Estimate genotyping error rate

Description

Estimate the genotyping error rates in SNP data, based on a pedigree and/or duplicates. Estimates probabilities (observed given actual) hom|other hom, het|hom, and hom|het.

Usage

EstEr(
  GenoM,
  Pedigree,
  Duplicates = NULL,
  Er_start = c(0.05, 0.05, 0.05),
  perSNP = FALSE
)

Arguments

GenoM	Genotype matrix
Pedigree	data.frame with columns id - dam - sire
Duplicates	matrix or data.frame with 2 columns, id1 & id2
Er_start	vector of length 3 with starting values for optim.
perSNP	logical, estimate error rate per SNP. WARNING not very precise, use only as an approximate indicator! Try on simulated data first, e.g. with SimGeno.

Details

The result should be interpreted as approximate, ballpark estimates! The estimated error rates from a pedigree will not be as accurate as from duplicate samples. Errors in individuals without parents or offspring will not be counted, and errors in individuals with only few offspring may not be noted either. Deviation of genotype frequencies among founders from Hardy-Weinberg equilibrium may wrongly be attributed to genotyping errors. Last but not least, any pedigree errors will result in higher estimated genotyping errors.

Value

vector of length 3 with estimated genotyping error rates: the probabilities that

• hom|hom: an actual homozygote is observed as the other homozygote

• het|hom: an actual homozygote is observed as heterozygote

• hom|het: an actual heterozygote is observed as homozygote

These are three independent parameters, that define the genotyping error matrix (see ErrToM) as follows:

	0	1	2
0	1-E_1-E_2	E_2	E_1
1	E_3	1-2E_3	E_3
2	E_1	E_2	1-E_1-E_2

Note that for optim a lower bound of 1e-6 and upper bound of 0.499 are used; if these values are returned this should be interpreted as 'inestimably small' and 'inestimably large', respectively.

Examples

GenoX <- SimGeno(Ped_griffin, nSnp=400, SnpError=c(0.01,0.07, 0.1),
                ParMis=0.1, CallRate=0.9)
EstEr(GenoM=GenoX, Pedigree=Ped_griffin)

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.