duplicateDiscordanceProbability: Probability of duplicate discordance
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/duplicateDiscordanceProbability.R

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

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

`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.

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.

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).

Cathy Laurie

duplicateDiscordance, duplicateDiscordanceAcrossDatasets

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]