PING_nucleosome_positions {consensusSeekeR} | R Documentation |
Nucleosome positions detected by the PING software using syntetic reads generated using a normal distribution with a variance of 20 for regions chr1:10000-15000.
data(PING_nucleosome_positions)
A GRanges
containing one entry per detected
nucleosome. The surronding ranges associated to those nucleosomes are in
the dataset PING_nucleosome_positions
.
Sangsoon W, Zhang X, Sauteraud R, Robert F and Gottardo R. 2013. PING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics 29 (16): 2049-50.
PING_nucleosome_ranges
the associate
genomic ranges dataset.
findConsensusPeakRegions
for extracting regions
sharing nucleosomes from more than one experiment.
## 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)