validatePrepMergeParameters {RJMCMCNucleosomes} | R Documentation

## Parameters validation for the `postMerge` function

### Description

Validation of all parameters needed by the public `postMerge` function.

### Usage

    validatePrepMergeParameters(reads, seqName, resultRJMCMC, extendingSize,
      chrLength)

### Arguments

`reads` | a `GRanges` containing all forward and reverse reads.The start positions of both reads are going to be used for the analysis. Beware that the start position of a reverse read is always higher that the end positition. The `GRanges` should at least contain one read.
`seqName` | a `character` string containing the label of the chromosome, present in the `GRanges` object, that will be used. The `NULL` value is accepted when only one seqname is present in the `GRanges`; the only seqname present will be used.
`resultRJMCMC` | an object of `class` "rjmcmcNucleosomes" or "rjmcmcNucleosomesMerge" that contain information about nucleosome positioning for an entire chromosome.
`extendingSize` | a positive `numeric` or a positive `integer` indicating the size of the consensus region used to group closeley positioned nucleosomes.The minimum size of the consensus region is equal to twice the value of the `extendingSize` parameter. The numeric will be treated as an integer.
`chrLength` | a positive `numeric` or a positive `integer` indicating the lenght of the current chromosome. The length of the chromosome is used to ensure that the consensus positions are all located inside the chromosome.

### Value

`0` indicating that all parameters validations have been successful.

### Author(s)

Astrid Deschenes

### Examples

    ## Load dataset containing forward and reverse reads
    data(reads_demo_01)

    ## Load dataset containing nucleosome information
    file_002 <- dir(system.file("extdata", package = "RJMCMCNucleosomes"),
    pattern = "RJMCMC_seg_02.RDS", full.names = TRUE)
    nucleosome_info <- readRDS(file_002)

    ## The function returns 0 when all parameters are valid
    RJMCMCNucleosomes:::validatePrepMergeParameters(reads = reads_demo_01,
    seqName = "chr_SYNTHETIC", resultRJMCMC = nucleosome_info,
    extendingSize = 74, chrLength = 10000000)

    ## The function raises an error when at least one paramater is not valid
    ## Not run: RJMCMCNucleosomes:::validatePrepMergeParameters(
    reads = c(72400, 72431, 72428, 72429, 72426),
    resultRJMCMC = NA, extendingSize = 74, chrLength = 10000000)
    ## End(Not run)

[Package RJMCMCNucleosomes version 1.12.0 Index]