transitionProbability {VanillaICE}R Documentation

Compute the transition probability

Description

Wrapper for computing the locus-specific transition probability

Usage

transitionProbability(chromosome, position, TAUP = 1e+08, chromosomeAnnotation, verbose = FALSE)

Arguments

chromosome chromosome (integer representation)
position physical position
TAUP Scalar for computing transition probabilities (see Details).
chromosomeAnnotation Optional: chromosome annotation
verbose Logical: verbose output

Details

The HMM uses locus-specific transition probabilities that are calculated as a function of the physical distance between loci. Specifically, the probability that the locus at position t-1 is not informative for the locus at position t is calculated as 1-exp(-d/TAUP), where d is the physical distance between locus t and locus t-1. The default for TAUP is 1 x 10^8 and can be specified to acheive a desired amount of sensitivity and specificity. Larger values of TAUP decreases the probability of transitioning to other states, and therefore provides a more smooth fit.

Value

The transitionProbability function (i) transforms the physical distance between adjacent loci to an estimate of the genomic distance and (ii) adds an 'arm' variable to the annotation matrix.

chromosome chromosome
position physical position
arm an integer. The HMM uses the arm variable as a factor and is fit independently to each 'arm'.
transitionPr locus-specific transition probabilities

Author(s)

R. Scharpf

See Also

chromosomeAnnotation


[Package VanillaICE version 1.6.0 Index]