segTable
A data.frame of segments, with at least "chrom", "start" and "end" columns. Standard behavior (default fun value) assumes "start" and "end" to be at least numeric, preferably integer.
fun
A list of functions, defining how to merge values when merging rows. It should contain an unamed element for the default function, and named elements to deal with specific columns.
factorsAsIntegers
Single logical value, whether to handle columns of class factor as integers or as is. Using TRUE dramatically shortens computation time in default user case ("chrom" column of class factor, "unique" function applied), but FALSE may be required to allow non-standard merging functions to access encoded values rather than factor indexes.