viterbi2GRanges {STAN} | R Documentation |
Convert the viterbi path to a GRanges object
viterbi2GRanges(viterbi, regions, binSize)
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. |
The viterbi path as GRanges object.
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)