Table 1.

GLANET main parameters for enrichment test

Association statistic options
EOO	Existence of overlap: Overlap statistic is 1 or 0 based on whether the input interval overlaps with any of the genomic element intervals or not.
NOOB	Number of overlapping bases: Overlap test statistic is the exact number of overlapping bases between the input interval and the genomic element intervals.
Random interval generation matching options
wGC	with GC: For an input interval, randomly sample an interval with the same length from the same chromosome such that it matches the GC content of the query interval.
wM	with mappability: Randomly sample an interval with the same length from the same chromosome such that it matches the mappability of the query interval.
wGCM	with GC and mappability: Randomly sample an interval with the same length from the same chromosome such that it matches both mappability and GC content of the query interval.
woGCM	without GC and mappability: Randomly sample an interval with the same length from the same chromosome.
Random interval generation start options
wIF	with isochore family: Starts the random interval search within the same chromosome with a matching GC isochore family. When GC is on, it provides a good start for GC matching. When GC option is not selected, it provides coarse grain GC matching.
woIF	without isochore family: Starts the random interval search for an interval within the chromosome randomly.