I'm using CNEr to detect CNEs in genomes of human and gar with 3 identities and 3 windows using ceScan.

identities <- c(45L, 48L, 49L)
windows <- c(50L, 50L, 50L)
CNEListHomoLepi <- ceScan(x=AxtHomoLepi, tFilter=BedHomo,
                          qFilter=BedLepi, tSizes=SizeHomo, qSizes=SizeLepi, 
                          window=windows, identity=identities)
CNEListLepiHomo <- ceScan(x=AxtLepiHomo, tFilter=BedLepi,
                          qFilter=BedHomo, tSizes=SizeLepi, qSizes=SizeHomo, 
                          window=windows, identity=identities)

As a result, the CNEList has 3 GrangePairs objects, each having numerous pairs and metadata columns. When I'm using CNE21() and CNE12(), the error returned:

Error: unable to find an inherited method for function 'CNE12'  for signature x = '"GRangePairs"'

The traceback is shown here:

3. stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), call. = FALSE, domain = NA)
2. (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L) ...
1. CNE12(CNEListHomoLepi[["45_50"]])

I'll appreciate it if anybody reply and give me advice to solve this problem. Thanks!