GWASTools (version 1.18.0)

duplicateDiscordanceProbability: Probability of duplicate discordance

Description

duplicateDiscordanceProbability calculates the probability of observing discordant genotypes for duplicate samples.

Usage

duplicateDiscordanceProbability(npair, error.rate = c(1e-5, 1e-4, 1e-3, 1e-2), max.disc = 7)

Arguments

npair

The number of pairs of duplicate samples.

error.rate

A numeric vector of error rates (i.e., the rate at which a genotype will be called incorrectly).

max.disc

The maximum number of discordances for which to compute the probability.

Value

This function returns a matrix of probabilities, where the column names are error rates and the row names are expected number of discordant genotypes (>0 through >max.disc).

Details

Since there are three possible genotypes, one call is correct and the other two are erroneous, so theoretically there are two error rates, a and b. The probability that duplicate genotyping instances of the same subject will give a discordant genotype is 2[(1 - a - b)(a + b) + ab]. When a and b are very small, this is approximately 2(a + b) or twice the total error rate. This function assumes that a == b, and the argument error.rate is the total error rate a + b.

Any negative values for the probability (due to precision problems for very small numbers) are set to 0.

See Also

duplicateDiscordance, duplicateDiscordanceAcrossDatasets

Examples

disc <- duplicateDiscordanceProbability(npair=10, error.rate=c(1e-6, 1e-4))

#probability of observing >0 discordant genotypes given an error rate 1e-6
disc[1,1]

#probability of observing >1 discordant genotypes given an error rate 1e-4
disc[2,2]