getDiffMeth {methInheritSim} | R Documentation |
Identify differentially methylated sites and among those, the ones
that are inherited.
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)
[Package
methInheritSim version 1.15.0
Index]