callPeaks {epigraHMM} | R Documentation |
This function imports the output from 'epigraHMM' and outputs a set of peaks (consensus or differential) for a given FDR control threshold or Viterbi sequence.
callPeaks( object, hdf5 = metadata(object)$output, method = "viterbi", saveToFile = FALSE, control = NULL )
object |
an epigraHMMDataSet |
hdf5 |
a character with the location of the epigraHMM HDF5 output file |
method |
either 'viterbi' or a numeric FDR control threshold (e.g. 0.05). Default is 'viterbi'. |
saveToFile |
a logical indicating whether or not to save the results to file. Output files are always saved with peaks of interest defined on the region level. Default is FALSE. |
control |
list of control arguments from controlEM(). This is an optional parameter and it is only required when 'saveToFile = TRUE' so that the output directory can be obtained. Default is NULL. |
A GRanges object with differential peak calls in BED 6+3 format
Pedro L. Baldoni, pedrobaldoni@gmail.com
https://github.com/plbaldoni/epigraHMM
# Creating dummy object countData <- rbind(matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1), matrix(rnbinom(2e3,mu = 7.5,size = 5),ncol = 1), matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1)) colData <- data.frame(condition = 'A', replicate = 1) rowRanges <- GenomicRanges::GRanges('chrA', IRanges::IRanges(start = seq(from = 1, length.out = 4e3,by = 250),width = 250)) object <- epigraHMMDataSetFromMatrix(countData,colData,rowRanges) # Initializing object <- initializer(object,controlEM()) # Running epigraHMM object <- epigraHMM(object,controlEM(),type = 'consensus',dist = 'nb') # Calling peaks peaks <- callPeaks(object = object, hdf5 = S4Vectors::metadata(object)$output, method = 'viterbi')