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

In ArnaudDroitLab/RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

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)

ArnaudDroitLab/RJMCMCNucleosomes documentation built on May 5, 2019, 7:06 a.m.