I would like to ask you a question regarding the behaviour of CopywriteR in the regions of very low coverage. In some cases, the results that I obtained from CopywriteR shows a number -1073741823.5​ (like below). I would like to confirm if this is in fact the result of very low read coverage of that region (which is the case here), hence it is a representation of -infinity as we're trying to calculate logarithm from around 0 or this number -1073741823.5 means something else.

chr6 28440001 28460000 chr6:28440001-28460000 -0.0591165718309049
chr6 28460001 28480000 chr6:28460001-28480000 -0.187528042663276
chr6 28480001 28500000 chr6:28480001-28500000 -1073741823.5
chr6 28500001 28520000 chr6:28500001-28520000 -1073741823.5
chr6 28520001 28540000 chr6:28520001-28540000 -1073741823.5

You are right that this represents a very low coverage. The output of CopywriteR is log2-transformed, and hence you would obtain -Inf if there is a coverage of 0. We replace those values by a (more or less randomly chosen) value of -.Machine$integer.max / 2 (i.e., the lowest possible integer value divided by 2). Although technically this would not be correct, it has a number of advantages (i.e., it allows for plotting in the igv browser and in our plotCNA function).