EstErr

Estimate genotyping error rate from Mendelian errors per SNP.

internal

Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.

Jisca Huisman

sequoia

Pedigree Inference from SNPs

EstErr function

<dl><dt>GenoM</dt>
<dd>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.</dd>
<dt>Par</dt>
<dd>pedigree dataframe, only genotyped parents are used.</dd>
<dt>ErrFlavour</dt>
<dd>function that takes the genotyping error rate <code>Err</code> 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 <code>ErrToM</code>.</dd></dl>

Arguments

Estimate Genotyping Error Rate — EstErr

<dl>

<dt>GenoM</dt>
<dd>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.</dd>


<dt>Par</dt>
<dd>pedigree dataframe, only genotyped parents are used.</dd>


<dt>ErrFlavour</dt>
<dd>function that takes the genotyping error rate <code>Err</code> 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 <code>ErrToM</code>.</dd>

</dl>

EstErr: Estimate Genotyping Error Rate

Description

Usage

Value

Arguments

See Also