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

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.

data(NucPosSimulator_nucleosome_ranges)

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


## 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)
#> $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 = 30, expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = TRUE, 
#>     minNbrExp = 2, nbrThreads = 1)
#> 
#> $consensusRanges
#> GRanges object with 27 ranges and 0 metadata columns:
#>        seqnames      ranges strand
#>           <Rle>   <IRanges>  <Rle>
#>    [1]     chr1 10002-10148      *
#>    [2]     chr1 10167-10314      *
#>    [3]     chr1 10334-10482      *
#>    [4]     chr1 10503-10649      *
#>    [5]     chr1 10670-10816      *
#>    ...      ...         ...    ...
#>   [23]     chr1 14177-14325      *
#>   [24]     chr1 14340-14488      *
#>   [25]     chr1 14506-14657      *
#>   [26]     chr1 14677-14824      *
#>   [27]     chr1 14842-14992      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "consensusRanges"

Format

References

See also

Examples