sequoia: CalcChi2 – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

CalcChi2

Chi-square Test on Observed vs Expected Genotypes

Description

For one SNP and all offspring-parent-parent trios or single parent-offspring pairs, calculate the expected genotype frequencies given the allele frequency, genotyping error rate, and error flavour, and perform a chi-square test.

Usage

CalcChi2(E, q, A.obs, ErrF)

Arguments

`E`	presumed genotyping error rate.
`q`	allele frequency.
`A.obs`	array of dim 4x4x4 with counts of joined offspring-parent-parent at the SNPs
`ErrF`	ErrFlavour; function that takes the genotyping error rate `Err` 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 `ErrToM`.

Value

The chisquare value of the test.

Examples

## Not run: 
E.hat <- numeric(ncol(GenoM))  # based on trio where possible
for (l in 1:ncol(GenoM)) {
		E.hat[l] <- stats::optimise(CalcChi2, interval=c(0,1), q=AF[l],
		                     A.obs=OO.trio[l,,,], ErrF=ErrF)$minimum
} 
## End(Not run)

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30