R: Split a 'GRanges' containing reads in a list of smaller...

segmentation {RJMCMCNucleosomes}

R Documentation

Split a `GRanges` containing reads in a list of smaller segments for the `rjmcmc` function.

Description

Split a GRanges of reads (as example, the reads from a chromosome) in a list of smaller GRanges sot that the rjmcmc function can be run on each segments.

Usage

segmentation(reads, zeta = 147, delta, maxLength)

Arguments

`reads`	a `GRanges`, the reads that need to be segmented.
`zeta`	a positive `integer` or `numeric`, the length of the nucleosomes. Default: 147.
`delta`	a positive `integer` or `numeric`, the accepted range of overlapping section between segments. The overlapping section being `zeta` + `delta`.
`maxLength`	a positive `integer` or `numeric`, the length of each segment.

Value

a GRangesList containing all the segments.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples


## Load synthetic dataset of reads
data(syntheticNucleosomeReads)

## Use dataset of reads to create GRanges object
sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr,
    ranges = IRanges(start = syntheticNucleosomeReads$dataIP$start,
    end = syntheticNucleosomeReads$dataIP$end),
    strand = syntheticNucleosomeReads$dataIP$strand)

# Segmentation of the reads
segmentation(reads = sampleGRanges, zeta = 147, delta = 50,
maxLength = 1000)

[Package RJMCMCNucleosomes version 1.4.0 Index]