validateRunSimOtherParameters: Parameters validation for the 'runSim' function. Only...

In belleau/methylInheritanceSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description

Validation of all parameters needed by the public runSim function. Only parameters other than double, integer and logical are validated.

Usage

validateRunSimOtherParameters(outputDir, fileID, methData, context, assembly)

Arguments

outputDir	a string of character or NULL, the path where the files created by the function will be saved. When NULL, the files are saved in the current directory.
fileID	a string of character, a identifiant that will be included in each output file name. Each output file name is composed of those elements, separated by "_": a type name, ex: methylGR, methylObj, etc.. a fileID the chromosome number, a number between 1 and nbSynCHR the number of samples, a number in the vNbSample vector the mean proportion of samples that has, for a specific position, differentially methylated values, a number in the vpDiff vector the proportion of C/T for a case differentially methylated that follows a shifted beta distribution, a number in the vDiff vector the proportion of cases that inherits differentially sites, a number in the vInheritance vector the identifiant for the simulation, a number between 1 and nbSimulation the file extension ".rds"
methData	an object of class methylBase, the CpG information from controls (CTRL) that will be used to create the sythetic chromosome. The methData object can also contain information from cases but only the controls will be used.
context	a string of character, the methylation context string, ex: CpG,CpH,CHH, etc.
assembly	a string of character, the short description of the genome assembly. Ex: mm9,hg18 etc.

Value

0 indicating that the function has been successful.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Load dataset
data("samplesForChrSynthetic")

## The function returns 0 when all paramaters are valid
methInheritSim:::validateRunSimOtherParameters(
outputDir = "test", fileID = "test", methData = samplesForChrSynthetic, 
context = "CpG", assembly = "Rnor_5.0")

belleau/methylInheritanceSim documentation built on April 1, 2020, 2:43 p.m.