## Loading datasets
data(PING_nucleosome_positions)
data(PING_nucleosome_ranges)
data(NOrMAL_nucleosome_positions)
data(NOrMAL_nucleosome_ranges)
data(NucPosSimulator_nucleosome_positions)
data(NucPosSimulator_nucleosome_ranges)
## Assigning experiment name to each row of the dataset.
## Position and range datasets from the same sofware must
## have identical names.
names(PING_nucleosome_positions) <- rep("PING",
length(PING_nucleosome_positions))
names(PING_nucleosome_ranges) <- rep("PING",
length(PING_nucleosome_ranges))
names(NOrMAL_nucleosome_positions) <-rep("NOrMAL",
length(NOrMAL_nucleosome_positions))
names(NOrMAL_nucleosome_ranges) <- rep("NOrMAL",
length(NOrMAL_nucleosome_ranges))
names(NucPosSimulator_nucleosome_positions) <-rep("NucPosSimulator",
length(NucPosSimulator_nucleosome_positions))
names(NucPosSimulator_nucleosome_ranges) <- rep("NucPosSimulator",
length(NucPosSimulator_nucleosome_ranges))
## Calculating consensus regions for chromosome 1
## with a default region size of 20 bp (2 * extendingSize).
## The consensus regions are not resized to fit genomic ranges of the
## included nucleosomes.
## Nucleosomes from at least 2 software must be present in a region to
## be retained as a consensus region.
chrList <- Seqinfo(c("chr1"), c(249250621), NA)
findConsensusPeakRegions(
narrowPeaks = c(PING_nucleosome_ranges,
NOrMAL_nucleosome_ranges,
NucPosSimulator_nucleosome_ranges),
peaks = c(PING_nucleosome_positions,
NOrMAL_nucleosome_positions,
NucPosSimulator_nucleosome_positions),
chrInfo = chrList,
extendingSize = 10,
expandToFitPeakRegion = FALSE,
shrinkToFitPeakRegion = FALSE,
minNbrExp = 3,
nbrThreads = 1)
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