trimClusters: Trims CpG clusters
In BiSeq: Processing and analyzing bisulfite sequencing data

Description Usage Arguments Details Value Author(s) References See Also Examples

CpG clusters rejected in a previous step are trimmed.

1	trimClusters(clusters.rej, FDR.loc)

`clusters.rej`	Output of `testClusters`.
`FDR.loc`	Location-wise FDR level. Default is 0.2.

Not differentially methylated CpG sites are removed within the CpG clusters rejected by testClusters.

A data.frame containing the differentially methylated CpG sites.

Katja Hebestreit

Yoav Benjamini and Ruth Heller (2007): False Discovery Rates for Spatial Signals. American Statistical Association, 102 (480): 1272-81.

testClusters

## 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)