# Estimate genotyping error rate (REMOVED; will be re-implemented)

`EstEr.Rd`

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. THESE ARE APPROXIMATE VALUES!

## 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`

.

## 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. PLEASE DO NOT USE
THESE VALUES AS INPUT IN SUBSEQUENT ANALYSIS BUT SUBSITUTE BY A SENSIBLE
VALUE!!

## 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.