My testing is telling me that for union region generation 1 is the default (a gap), not -1 (1bp overlap). Negative numbers are decreasing as expected, but I am unsure about what the 1bp gap as a default represents. Does a default of mergeOverlap = 1 mean that regions will be merged if they overlap or are up to 1bp away from each other?

Thank you, Ian

This is the default where config$mergeOverlap = NULL (how it is without me changing anything) 9 Samples, 134545 sites in matrix (183389 total)

samples_qval <- dba(sampleSheet="sample_sheet_qval.csv", minOverlap=2)

This is where config$mergeOverlap = 1. 9 Samples, 134545 sites in matrix (183389 total) = same as above.

samples_qval_1bp <- dba(sampleSheet="sample_sheet_qval.csv", minOverlap=2)
samples_qval_1bp$config$mergeOverlap <- 1
samples_qval_1bp <- dba(samples_qval_1bp)

This is where config$mergeOverlap = -1. 9 Samples, 134406 sites in matrix (182919 total):

samples_qval_m1bp <- dba(sampleSheet="sample_sheet_qval.csv", minOverlap=2)
samples_qval_m1bp$config$mergeOverlap <- -1
samples_qval_m1bp <- dba(samples_qval_m1bp)

This is where config$mergeOverlap = -60. 9 Samples, 130414 sites in matrix (171033 total)

samples_qval_30pc <- dba(sampleSheet="sample_sheet_qval.csv", minOverlap=2)
samples_qval_30pc$config$mergeOverlap <- -60
samples_qval_30pc <- dba(samples_qval_30pc)