BiSeq (version 1.12.0)

trimClusters: Trims CpG clusters

Description

CpG clusters rejected in a previous step are trimmed.

Usage

trimClusters(clusters.rej, FDR.loc)

Arguments

clusters.rej

Output of testClusters.

FDR.loc

Location-wise FDR level. Default is 0.2.

Value

data.frame containing the differentially methylated CpG sites.

Details

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

References

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

See Also

testClusters

Examples

## 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)