validatePlotNucleosomesParameters: Parameters validation for the 'plotNucleosomes' 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 plotNucleosomes function.

Usage

validatePlotNucleosomesParameters(nucleosomePositions, reads, seqName, xlab,
  ylab, names)

Arguments

nucleosomePositions	a GRanges or a GRangesList containing the nucleosome positions for one or multiples predictions obtained using the same reads. In presence of only one prediction (with multiples nucleosome positions), a GRanges is used. In presence of more thant one predictions (as example, before and after post-treatment or results from different software), a GRangesList with one entry per prediction is used.
reads	a GRanges containing forward and reverse reads. The GRanges should contain at least 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.
xlab	a character string containing the label of the x-axis.
ylab	a character string containing the label of the y-axis.
names	a vector of a character string containing the label of each prediction set. The vector must be the same length of the nucleosomePositions list or 1 in presence of a vector.

Value

0 indicating that all parameters validations have been successful.

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

## Load GRanges dataset
data(reads_demo_01)

## Load RJMCMC result
data(RJMCMC_result)

## The function returns 0 when all parameters are valid
RJMCMCNucleosomes:::validatePlotNucleosomesParameters(nucleosomePositions =
RJMCMC_result$mu, reads = reads_demo_01, seqName = "chr_SYNTHETIC",
xlab = "position", ylab = "coverage", names = c("test"))

## The function raises an error when at least one paramater is not valid
#\dontrun{RJMCMCNucleosomes:::validatePlotNucleosomesParameters(
#nucleosomePositions = c("hi"), reads = reads,
#xlab = "position", ylab = "coverage", names = c("test"))}

#\dontrun{RJMCMCNucleosomes:::validatePlotNucleosomesParameters(
#nucleosomePositions = RJMCMC_result$mu, reads = reads_demo_01,
#seqName = "chr_SYNTHETIC", xlab = "position", ylab = "coverage",
#names = c("test_one", "test_false"))}

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