validatePrepMergeParameters: Parameters validation for the 'postMerge' function

In ArnaudDroitLab/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 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)

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