This is part of code in   cn.mops:::referencecn.mops

                        ir <- c(ir,IRanges(start(inputChr)[
                                                segDfSubsetChr$start],
                                        end(inputChr)[segDfSubsetChr$end]))
                        irCNVR <- c(irCNVR,IRanges(start(inputChr)[
                                                start(cnvrRChr)],
                                        end(inputChr)[end(cnvrRChr)]))

  I tried very hard to understand, but this is just impossible for me. I asked developer, but couldn't get response.

  inputChr is GRanges object, segDfSubsetChr is data frame.

  In any case, start and end are chromosome location. How can these be used as index for vector?