Replication domain boundary calling

DefineRDBs(x, Slope_E = 2.75e-6, Slope_L = 1e-06, Ends = 1e6,
Data_Points = 30, Length_Max = 1e6, Length_Min = 2e5, RTU_Min = 0.55,
Span = 35, Gap = 8e4, Gap_Dis = 125e3)

# x - table with columns "CHR" and "POSITION" indicating genomic
coordinates of data points and additional columns containing replication
timing data from individual samples
# Slope_E - slope threshold for early Timing Transition Region (TTR)
borders
# Slope_L - slope threshold for late TTR borders
# Ends - minimum distance between early TTR borders and chromosome ends
# Data_Points - minimum number of data points within TTRs
# Length_Max - maximum TTR size
# Length_Min - minimum TTR size
# RTU_Min - minimum RT difference across TTR
# Span - span for loess smoothing
# Gap - threshold to define gaps in data point spacing
# Gap_Dis - minimum distance between early TTR borders and gaps in data
point spacing