Given a vector of CN values, detect and summarize lengths of any oscillating chains that are present in the sequence, along with 0s for non-oscillating sets.
Arguments
- cn_vals
vector of ints. Segment state values. Ideally from the chromosome of 1 sample.
- middle_bound
int|Inf. Default 2. How different the middle CN is allowed to be from either side to count as an oscillation. See extract_oscillations for a discussion of this. Default of 2 means the middle CN must be within 2 copy values of the flanking segments.
- ends_bound
int. Default 0. How different the ends of a 3-segment set are allowed to be to count as an oscillation
Details
A full discussion of this function can be found in the documentation of. extract_oscillations.
Examples:
3-2-3 = 1
1-2-3 = 0
3-2-3-1-2-3 = 1 0
3-2-3-2 = 2
3-2-3-2-1 = 2 0