minimum number of probes to be called a bound region.
asCherList
If TRUE, result is returned as class cherList. See Ringo, for further description.
Details
The function returns two objects, cmarrt.bound and indep.bound. Each object is a list of bound regions which can be accessed by $chr (chromosome), $peak.start (start coordinate of each bound region), $peak.stop (stop coordinate of each bound region),
$n.probe (number of probes within each bound region), $min.pv (minimum p-values of each bound region), $ave.pv (average p-values of each bound region).
Value
cmarrt.bound
list of bound regions obtained under correlation structure.
indep.bound
list of bound regions obtained under independence (ignoring correlation).
Note
The list of bound regions obtained under independence (ignoring the correlation structure) is for comparison. It is not recommended to use this list for downstream analysis.
Author(s)
Pei Fen Kuan, Adam Hinz
References
P.F. Kuan, H. Chun, S. Keles (2008). CMARRT: A tool for the analysiz of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pacific Symposium of Biocomputing13:515-526.