getDiffMeth: Identify differentially methylated sites and among those, the...

Description Usage Arguments Value Author(s) Examples

View source: R/methylInheritanceSimInternalMethods.R

Description

Identify the site positions where the cases are differentially methylated and, among those, the one that are inherited.

Usage

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getDiffMeth(stateInfo, rateDiff, minRate, propInherite, c = 1, b = -0.1,
  endLength = 1000)

Arguments

stateInfo

a GRanges that contains the CpG (or methylated sites). The GRanges have four metadata from the real dataset:

  • chrOri, the chromosome from the real dataset

  • startOri, the position of the site in the real dataset

  • meanCTRL, the mean of the control in the real dataset

  • varCTRL, the variance of the control in the real dataset

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 for differentially methylated sites.

propInherite

a non-negative double inferior or equal to 1, the proportion of differentially methylated regions that are inherated.

c

a positive double, a factor in the formula to compute the probabylity of site to be diffentially methylated in a differentially methylated region. The probability formula of site in differentially methylated region is c * exp(b * log(distance with the preceding sites)) Default: 1.0.

b

a negative double, a factor in the formula to compute the probabylity of site to be diffentially methylated in a differentially methylated region. The probability formula of site in differentially methylated region is c * exp(b * log(distance with the preceding sites)). Default: -1e-01.

endLength

a positive integer, when the distance with the preceding sites in a differentially methylated region is larger than endLength, the differentially methylated region is finished. Default: 1000.

Value

a list containing the 2 following elements:

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

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## Load dataset containing a list of objects used by 
## methInheritSim internal functions
data(dataSimExample)

## Identify differentially methylated sites and among those, the ones
## that are inherited
methInheritSim:::getDiffMeth(stateInfo = 
    dataSimExample$stateInfo, rateDiff = 0.3, minRate = 0.3,
    propInherite = 0.3)

belleau/methInheritSim documentation built on Dec. 4, 2018, 8:01 a.m.