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Maximum Number of Mismatches

CalcMaxMismatch.Rd

Calculate the maximum expected number of mismatches for duplicate samples, parent-offspring pairs, and parent-parent-offspring trios.

Usage

CalcMaxMismatch(Err, MAF, ErrFlavour = "version2.9", qntl = 1 - 1e-05)

Arguments

Err

estimated genotyping error rate, as a single number or 3x3 matrix (averaged value(s) across SNPs), or a vector with the same length as MAF, or a nSnp x 3 x 3 array. 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 an array, each 3x3 slice should abide this rule.

MAF

vector with minor allele frequency at each SNP.

ErrFlavour

function that takes 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'. Ignored if Err is a matrix. See ErrToM.

qntl

quantile of binomial distribution to be used as the maximum, of individual-level probability. For a desired dataset-level probability quantile \(Q\), use qntl\(= Q^{(1/N)}\), where \(N\) is the number of individuals.

Value

A vector with three integers:

DUP

Maximum number of differences between 2 samples from the same individual

OH

Maximum number of Opposing Homozygous SNPs between a true parent-offspring pair

ME

Maximum number of Mendelian Errors among a true parent-parent- offspring trio

.

Details

The thresholds for maximum number of mismatches calculated here aim to minimise false negatives, i.e. to minimise the chance that any true duplicates or true parent-offspring pairs are already excluded during the filtering steps where these MaxMismatch values are used. Consequently, there is a high probability of false positives, i.e. it is likely that some sample pairs with fewer mismatches than the MaxMismatch threshold, are in fact not duplicate samples or parent-offspring pairs. Use of these MaxMismatch thresholds is therefore only the first step of pedigree reconstruction by sequoia.

See also

SnpStats.

Examples

CalcMaxMismatch(Err = 0.05, MAF = runif(n=100, min=0.3, max=0.5))
#> DUP  OH  ME 
#>  24   8  14 
if (FALSE) {
CalcMaxMismatch(Err = 0.02, MAF = SnpStats(MyGenoMatrix, Plot=FALSE)[,"AF"])
}