sequoia (version 2.5.6)

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)

Value

The chisquare value of the test.

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.

See Also

EstErr, SnpStats.

Examples

if (FALSE) {
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
} }