Last seen 2.2 years ago
I would start by reading the Details section of the bumphunter help file.
Regarding the table, each row is a candidate DMR.
value - is the average of the estimated coefficient (usually representing the difference between two groups) in the region
area - is the absolute value of the sum of the estimated coefficients in the region
cluster - the genome is divided into smaller regions, called clusters. We search for regions in each cluster to avoid going over a long stretch of the genome with no data. The value provided here is the ID for the cluster.
indexStart - is the index of the probe in the original methylation matrix where the region starts
indexEnd- is the index of the probe in the original methylation matrix where the region ends
L - is the number of probes in the region
clusterL - number of probes in the cluster
p.value - are explained in the help file. These do need multiple comparison corrections.
fwer - are explained in the help file. These do not need multiple comparison corrections