NOrMAL_nucleosome_ranges: Ranges associated to nucleosomes detected by the NOrMAL...

In ArnaudDroitLab/consensusSeekeR: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Description

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

Usage

data(NOrMAL_nucleosome_ranges)

Format

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

References

• Polishko A, Ponts N, Le Roch KG and Lonardi S. 2012. NOrMAL: Accurate nucleosome positioning using a modified Gaussian mixture model. Bioinformatics 28 (12): 242-49.

See Also

• NOrMAL_nucleosome_positions the associate genomic positions dataset.

• findConsensusPeakRegions for extracting regions sharing nucleosomes from more than one experiment.

Examples

## 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 30 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 = 15,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = TRUE,
    minNbrExp = 2,
    nbrThreads = 1)

ArnaudDroitLab/consensusSeekeR documentation built on Feb. 6, 2020, 6:45 p.m.