NOrMAL_nucleosome_positions: Nucleosome positions detected by the NOrMAL software using...

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

Description

Nucleosome positions 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_positions)

Format

A GRanges containing one entry per detected nucleosome. The surronding ranges associated to those nucleosomes are in the dataset NOrMAL_nucleosome_ranges.

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_ranges the associate genomic ranges 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 40 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 = 20,
    expandToFitPeakRegion = TRUE,
    shrinkToFitPeakRegion = FALSE,
    minNbrExp = 3,
    nbrThreads = 1)

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