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

Source: R/consensusSeekeR.R

Ranges associated to nucleosomes 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_ranges)

Format

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

References

  • 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.

See also

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 20 bp (2 * extendingSize).
## which is not extended to include all genomic regions for the closest
## peak to the median position of all peaks included in the region (for
## each experiment).
## 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 = 2,
    nbrThreads = 1)
#> $call
#> 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 = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 27 ranges and 0 metadata columns:
#>        seqnames      ranges strand
#>           <Rle>   <IRanges>  <Rle>
#>    [1]     chr1 10065-10085      *
#>    [2]     chr1 10231-10251      *
#>    [3]     chr1 10397-10417      *
#>    [4]     chr1 10566-10586      *
#>    [5]     chr1 10733-10753      *
#>    ...      ...         ...    ...
#>   [23]     chr1 14241-14261      *
#>   [24]     chr1 14404-14424      *
#>   [25]     chr1 14571-14591      *
#>   [26]     chr1 14740-14760      *
#>   [27]     chr1 14906-14926      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"