initializer {epigraHMM} | R Documentation |
This function call enriched windows individually for each sample in an epigraHMMDataSet. These are then used for initializing purposes in epigraHMM. By default, the Viterbi algorithm is used to determine enriched windows. Input controls and normalizing offsets are not utilized in this initialization step.
initializer(object, control)
object |
an epigraHMMDataSet |
control |
list of control arguments from controlEM() |
To be added
An epigraHMMDataSet with a 'peaks' assay filled in.
Pedro L. Baldoni, pedrobaldoni@gmail.com
https://github.com/plbaldoni/epigraHMM
# Creating dummy object countData <- rbind(matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1), matrix(rnbinom(2e3,mu = 7.5,size = 5),ncol = 1), matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1)) colData <- data.frame(condition = 'A', replicate = 1) object <- epigraHMMDataSetFromMatrix(countData,colData) # Initializing object <- initializer(object,controlEM()) # Visualizing initialization peaks #plot(assay(object),type = 'l') #lines(7.5*assay(object,'peaks'),col = 'red')