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STAN (version 2.0.3)

viterbi2GRanges: Convert the viterbi path to a GRanges object

Description

Convert the viterbi path to a GRanges object

Usage

viterbi2GRanges(viterbi, regions, binSize)

Arguments

viterbi
A list containing the viterbi paths as factors. The output from getViterbi.
regions
GRanges object of the regions (e.g. chromosomes) stored in the viterbi path.
binSize
The bin size of the viterbi path.

Value

The viterbi path as GRanges object.

Examples

Run this code
library(GenomicRanges) 
data(yeastTF_databychrom_ex)
nStates = 6
dirobs = as.integer(c(rep(0,10), 1, 1))
bdhmm_gauss = initBdHMM(yeastTF_databychrom_ex, nStates, "Gaussian", directedObs=dirobs)
bdhmm_fitted_gauss = fitHMM(yeastTF_databychrom_ex, bdhmm_gauss)
viterbi_bdhmm_gauss = getViterbi(bdhmm_fitted_gauss, yeastTF_databychrom_ex)
yeastGRanges = GRanges(IRanges(start=1214616, end=1225008), seqnames="chrIV")
names(viterbi_bdhmm_gauss) = "chrIV"
viterbi_bdhmm_gauss_gr = viterbi2GRanges(viterbi_bdhmm_gauss, yeastGRanges, 8)

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