viterbi2GRanges: Convert the viterbi path to a GRanges object

In STAN: The Genomic STate ANnotation Package

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

library(GenomicRanges) 
data(yeastTF_databychrom_ex)
dStates = 6
dirobs = as.integer(c(rep(0,10), 1, 1))
bdhmm_gauss = initBdHMM(yeastTF_databychrom_ex, dStates = dStates, method ="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)

STAN documentation built on Nov. 8, 2020, 11:11 p.m.