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

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

Description

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

Usage

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:

• stateDiff a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG sites are differentially methylated.

• stateInherite a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG values are inherited.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

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