rcpp_viterbi {srnadiff}R Documentation

Run the Viterbi algorithm on the HMM.

Description

Run the Viterbi algorithm on the HMM.

Usage

rcpp_viterbi(chromosomeSizes, transitions, emissions, emissionThreshold, starts,
  counts, pvalues, lengths, values, minDepth, minSize, maxSize)

Arguments

chromosomeSizes

the sizes of the chromosomes

transitions

the transition log-probabilities

emissions

the emission log-probabilities

emissionThreshold

the emission threshold

starts

the start log-probabilities

counts

the unique counts

pvalues

the p-values of the counts

lengths

the sizes of the RLEs (one list per chromosome)

values

the values of the RLEs (one list per chromosome)

minDepth

the minimum read coverage

minSize

the minimum size region

maxSize

the maximum size region

Value

a segmentation of the chromosomes


[Package srnadiff version 1.0.0 Index]