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

Description Usage Format References See Also Examples

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

1

Format

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

References

See Also

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
## 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 Sept. 2, 2017, 8:25 p.m.