validateSegmentationParameters: Parameters validation for the 'segmentation' function

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

Description

Validation of all parameters needed by the public segmentation function.

Usage

validateSegmentationParameters(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

0 indicating that all parameters validations have been successful.

Author(s)

Astrid Deschenes, Pascal Belleau

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)

## The function returns 0 when all parameters are valid
RJMCMCNucleosomes:::validateSegmentationParameters(reads = sampleGRanges,
zeta = 147, delta = 30, maxLength = 12000)

## The function raises an error when at least one paramater is not valid
#\dontrun{RJMCMCNucleosomes:::validateSegmentationParameters(
#reads = c(100), zeta = 147, delta = 30, maxLength = 12000)}

#\dontrun{RJMCMCNucleosomes:::validateSegmentationParameters(
#reads = sampleGRanges, zeta = "hi", delta = 30, maxLength = 12000)}

RJMCMCNucleosomes documentation built on Nov. 8, 2020, 8:20 p.m.