validateSegmentationParameters {RJMCMCNucleosomes} | R Documentation

## Parameters validation for the `segmentation` function

### 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)}

[Package RJMCMCNucleosomes version 1.18.0 Index]