genomicDistance {VanillaICE}R Documentation

A rough estimate of the genomic distance between SNPs

Description

Calculates the genomic distance between SNPs as a function of the physical distance. This distance is used for calculating transition probabilities in the viterbi algorithm.

Usage

genomicDistance(object)
tau(object)
genomicDistance(object) <- value

Arguments

object An object inheriting from HmmOptions
value A vector of length T - 1, where T is the number of SNPs

Details

The genomic distance is calculated as exp(-2*d), where d is the physical distance in 100MB units.

In the Viterbi algorithm, the probability of remaining in state S at SNP t+1 is the genomic distance. The probability of transitioning to one of the alternative states is 1 - the genomic distance. The transitionScale function can be used to give more weight to transitioning back to the baseline ('normal') state.

Value

A numeric vector with length T-1.

Author(s)

R. Scharpf

See Also

transitionScale


[Package VanillaICE version 1.4.0 Index]