trimClusters {BiSeq} | R Documentation |
CpG clusters rejected in a previous step are trimmed.
trimClusters(clusters.rej, FDR.loc)
clusters.rej |
Output of |
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.
## 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)