This release introduces the --bridge-gaps parameter to methscan scan and methscan diff.
By default, methscan scan runs a sliding window along the genome. Overlapping windows exceeding a certain variance threshold are then merged in a peak-calling procedure, yielding VMRs of variable size depending on the width of the variance peak. If there are long stretches of variably methylated DNA, this peak-calling can sometimes produce "fragmented VMRs", i.e. many nearby VMRs that are separated by very small gaps:
In this illustration, many VMRs (thick vertical purple lines) were detected in the gene body of the depicted gene. Since some of these VMRs are only separated by a tiny gap, it may be more appropriate to merge them into one continuous, large VMR.
This VMR merging is now possible by setting --bridge-gaps to e.g. 1000, which would mean that VMRs with a gap of 1000 bp or less will be merged into one VMR, as illustrated here on some mock data:
(red thick line: regular VMR peak calling; blue thick line: VMR peak calling with --bridge-gaps 400. The variance threshold is at 0.55; the y position of the thick lines has no meaning).
The same functionality was also added to the DMR detection approach implemented in methscan diff.
This release also fixes a minor bug in the calculation of the adjusted p-values associated with DMRs.