validateRJMCMCParameters: Parameters validation for the 'rjmcmc' 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 rjmcmc function.

Usage

validateRJMCMCParameters(reads, seqName, nbrIterations, kMax, lambda,
  minInterval, maxInterval, minReads, adaptIterationsToReads, vSeed)

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.
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.
nbrIterations	a positive integer or numeric, the number of iterations. Non-integer values of nbrIterations will be casted to integer and truncated towards zero.
kMax	a positive integer or numeric, the maximum number of nucleosomes per region. Non-integer values of kMax will be casted to integer and truncated towards zero.
lambda	a positive numeric, the theorical mean of the Poisson distribution.
minInterval	a numeric, the minimum distance between two nucleosomes.
maxInterval	a numeric, the maximum distance between two nucleosomes.
minReads	a positive integer or numeric, the minimum number of reads in a potential canditate region. Non-integer values of minReads will be casted to integer and truncated towards zero.
adaptIterationsToReads	a logical indicating if the number of iterations must be modified in function of the number of reads.
vSeed	a integer. A seed used when reproducible results are needed. When a value inferior or equal to zero is given, a random integer is used.

Value

0 indicating that all parameters validations have been successful.

Author(s)

Astrid Deschenes

Examples

reads <- GRanges(seqnames = Rle(c("chr1"), c(10)),
    ranges = IRanges(101:110, end = 111:120, names = head(letters, 10)),
    strand = Rle(strand(c("-", "+", "-", "+", "-")), c(1, 2, 2, 3, 2)))

## The function returns 0 when all paramaters are valid
RJMCMCNucleosomes:::validateRJMCMCParameters(reads = reads,
seqName = "chr1", nbrIterations = 2, kMax = 10, lambda = 1, minReads = 1,
minInterval = 100, maxInterval = 200, adaptIterationsToReads = TRUE,
vSeed = 100)

## The function raises an error when at least one paramater is not valid
## Not run: RJMCMCNucleosomes:::validateRJMCMCParameters(
reads = NA, seqName = "chr1",
nbrIterations = 2, kMax = 10, lambda = 1, minReads = 1, minInterval = 100,
maxInterval = 200, adaptIterationsToReads = TRUE, vSeed = -1)
## End(Not run)

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