Description Usage Arguments Value Author(s) See Also Examples
This function aggregates CpG sites to DMRs on the basis of their P values.
1  findDMRs(test.out, alpha, max.dist, diff.dir)

test.out 
An object returned by 
alpha 
OPTIONAL. A DMR contains CpG sites with P values smaller or equal than 
max.dist 
Numeric. The maximum distance between two P values smaller than

diff.dir 
Logical. Should DMRs be seperated if the direction of methylation
differences changes? If 
A GRanges
object storing the start and end positions of the DMRs with information in metadata columns:
median.p 
median of P values 
median.meth.group1 
median of modeled methylation level of group1. 
median.meth.group1 
median of modeled methylation level of group2. 
median.meth.diff 
median of difference of modeled methylation levels of group1 and group2. 
Katja Hebestreit
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  ## Variogram under Null hypothesis (for resampled data):
data(vario)
plot(vario$variogram$v)
vario.sm < smoothVariogram(vario, sill=0.9)
# auxiliary object to get the pValsList for the test
# results of interest:
data(betaResults)
vario.aux < makeVariogram(betaResults, make.variogram=FALSE)
# Replace the pValsList slot:
vario.sm$pValsList < vario.aux$pValsList
## vario.sm contains the smoothed variogram under the Null hypothesis as
## well as the p Values that the group has an effect on DNA methylation.
locCor < estLocCor(vario.sm)
clusters.rej < testClusters(locCor, FDR.cluster = 0.1)
clusters.trimmed < trimClusters(clusters.rej, FDR.loc = 0.05)
DMRs < findDMRs(clusters.trimmed, max.dist=100, diff.dir=TRUE)

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