validateRunSimDoubleParameters: Parameters validation for the 'runSim' function. Only double...

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

Description

Validation of all parameters needed by the public runSim function. Only double parameters are validated.

Usage

validateRunSimDoubleParameters(vpDiff, vpDiffsd, vDiff, vInheritance,
  propInherite, rateDiff, minRate, propHetero, maxPercReads)

Arguments

vpDiff	a double superior to 0 and inferior or equal to 1, the mean value for the proportion of samples that will have, for a specific position, differentially methylated values. It can be interpreted as the penetrance.
vpDiffsd	a non-negative double, the standard deviation associated to the propDiff.
vDiff	a positive double between [0,1], the proportion of C/T for a case differentially methylated follow a beta distribution where the mean is shifted of vDiff from the CTRL distribution
vInheritance	a positive double between [0,1], the proportion of cases that inherited differentially sites.
propInherite	a non-negative double inferior or equal to 1, the proportion of differentially methylated site are inherated
rateDiff	a positive double inferior to 1, the mean of the chance that a site is differentially methylated.
minRate	a non-negative double inferior to 1, the minimum rate of differentially methylated sites.
propHetero	a positive double between [0,1], the reduction of vDiff for the second and following generations.
maxPercReads	a double between [0,100], the percentile of read counts that is going to be used as upper cutoff. Bases ore regions having higher coverage than this percentile are discarded. Parameter used for both CpG sites and tiles analysis. The parameter correspond to the hi.perc parameter in the methylKit package.

Value

0 indicating that the function has been successful.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## The function returns 0 when all paramaters are valid
methInheritSim:::validateRunSimDoubleParameters(vpDiff =0.2, 
vpDiffsd = 0.3, vDiff = 0.4, vInheritance = 0.2, propInherite = 0.5, 
rateDiff = 0.2, minRate = 0.1, propHetero = 0.2, maxPercReads = 99.1)

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