NucPosSimulator_nucleosome_ranges: Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.

Description

Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution with a variance of 20 for regions chr1:10000-15000.

Usage

data(NucPosSimulator_nucleosome_ranges)

Arguments

Format

A GRanges containing one entry per detected nucleosome. The ranges are surronding the nucleosomes present in the dataset NucPosSimulator_nucleosome_positions. The genomic ranges have been obtained by adding 73 bps on each side of the detected positions.

References

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.

Examples

Run this code


## 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 60 bp (2 * extendingSize).
## Consensus regions are resized to include all genomic regions of
## 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 = 30,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = TRUE,
    minNbrExp = 2,
    nbrThreads = 1)