sequoia: ErrToM – R documentation

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ErrToM

Generate Genotyping Error Matrix

Description

Generate a matrix with the probabilities of observed genotypes (columns) conditional on actual genotypes (rows), or return a function to generate such matrices (using a single value Err as input to that function).

Usage

ErrToM(Err = NA, flavour = "version2.0", Return = "matrix")

Arguments

`Err`	estimated genotyping error rate, as a single number or 3x3 or 4x4 matrix. If a single number, an error model is used that aims to deal with scoring errors typical for SNP arrays. If a matrix, this should be the probability of observed genotype (columns) conditional on actual genotype (rows). Each row must therefore sum to 1. If `Return='function'`, this may be `NA`.
`flavour`	matrix-generating function, or one of 'version2.0', 'version1.3' (='SNPchip'), 'version1.1' (='version111'), referring to the sequoia version in which it was used as default. Ignored if `Err` is a matrix and `Return='matrix'` (in which case the matrix will only be checked for validity).
`Return`	output, 'matrix' (always 3x3) or 'function'.

Details

By default (flavour = "SNPchip"), Err is interpreted as a locus-level error rate (rather than allele-level), and equals the probability that an actual heterozygote is observed as either homozygote (i.e., the probability that it is observed as AA = probability that observed as aa = Err/2). The probability that one homozygote is observed as the other is (Err/2)^2.

The inbuilt 'flavours' correspond to the presumed and simulated error structures, which have changed with sequoia versions. The most appropriate error structure will depend on the genotyping platform; 'version0.9' and 'version1.1' were inspired by SNP array genotyping while 'version1.3' and 'version2.0' are intended to be more general.

Pr(observed genotype (columns) | actual genotype (rows)):

version2.0:

	0	1	2
0	(1-E/2)^2	E(1-E/2)	(E/2)^2
1	E/2	1-E	E/2
2	(E/2)^2	E(1-E/2)	(1-E/2)^2

version1.3

	0	1	2
0	1-E-(E/2)^2	E	(E/2)^2
1	E/2	1-E	E/2
2	(E/2)^2	E	1-E-(E/2)^2

version1.1

	0	1	2
0	1-E	E/2	E/2
1	E/2	1-E	E/2
2	E/2	E/2	1-E

version0.9 (not recommended)

	0	1	2
0	1-E	E	0
1	E/2	1-E	E/2
2	0	E	1-E

Value

Either a 3x3 matrix, or a function generating a 3x3 matrix.

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30