getControlIndex:
Get indices of control probes from CpG-free regions
Description
Get indices of control probes from CpG-free regions.
Usage
getControlIndex(dat, controlProbes = NULL, noCpGWindow = 1000, subject, onlyGood = FALSE, matrix = TRUE)
Arguments
controlProbes
vector of names used to denote control probes in the 'container' column of the Nimblegen annotation (ndf) file. Optional
noCpGWindow
Size of the window centered on the probe that must be CpG-free
subject
A BSgenome object
onlyGood
deprecated option
Details
The probes can either be identified as control probes in the microarray annotation package, or alternatively the function will search the genome (given an appropriate BSgenome object) for suitable probes.