Preps segments for LGA call.

Does many things, details found within function body. First, assigns segments that meet certain criteria an index of 0 (there's 4 cases + edge cases for assigning an index of 0, inside the inner for-loop.) Then, removes the segments that were assigned this index of 0. They're considered "small breaks".

Usage

BreakSmoothToLGA(threshold, segments, granges_obj)

Arguments

threshold

A float. Threshold in ratio_median difference previously estimated.

segments

A data frame: segment data that's (ideally) already been processed (merging segments, small ones have been reinserted, and so on)

granges_obj

A GRanges object.