genomicDistance {VanillaICE} | R Documentation |
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.
genomicDistance(object) tau(object) genomicDistance(object) <- value
object |
An object inheriting from HmmOptions |
value |
A vector of length T - 1, where T is the number of SNPs |
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.
A numeric vector with length T-1.
R. Scharpf