NucPosSimulator_nucleosome_positions {consensusSeekeR} | R Documentation |
Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution with a variance of 20 for regions chr1:10000-15000.
data(NucPosSimulator_nucleosome_positions)
A GRanges
containing one entry per detected
nucleosome. The surronding ranges associated to those nucleosomes are in
the dataset NucPosSimulator_nucleosome_ranges
.
Schöpflin R, Teif VB, Müller O, Weinberg C, Rippe K, and Wedemann G. 2013. Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics 29 (19): 2380-86.
NucPosSimulator_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 50 bp (2 * extendingSize). ## The consensus regions are extended to include all genomic regions for ## all nucleosomes. However, if the consensus regions are larger than the ## genomic regions of the nucleosomes, the consensus regions are not ## shrinked. ## Nucleosomes from all 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 = 25, expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = FALSE, minNbrExp = 3, nbrThreads = 1)