epigraHMM {epigraHMM} | R Documentation |
This function runs either consensus (one condition, multiple samples) or differential (multiple conditions and samples) peak callers for epigenomic data.
epigraHMM(object, control, type, dist = "nb")
object |
an epigraHMMDataSet |
control |
list of control arguments from |
type |
character, either |
dist |
character, either |
An epigraHMMDataSet object with the results from epigraHMM
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()) # Running epigraHMM object <- epigraHMM(object,controlEM(),type = 'consensus',dist = 'nb')