IGENT: efficient entropy based algorithm for genome-wide gene-gene interaction analysis

BMC Medical Genomics

Table 1 Computation time of IGENT, BOOST, MDR, RF, and SVM.

SNP size	IGENT_exhaust	BOOST	MDR	RF	SVM
50	<1s	<1s	1s	11s	13s
100	<1s	<1s	4s	46s	53s
500	<1s	<1s	1m 8s	20m	23m
1K	3s	1s	4m 25s	1h 15m	1h 29m
2K	8s	6s	19m 52s	5h	5h 50m
5K	38s	30s	2h 4m	1d 6h	1d 12h
10K	2m 34s	2m 7s	*8h 16m	*5d 5h	*6d 3h
100K	4h 23m	3h 32m	*35d	*520d	*614d
350K	2d 4h	1d 19h	*422d	*6366d	*7524d
500K	4d 10h	3d 15h	*861d	*12992d	*15353d

Computation time is measured in simulation 1 dataset which have 2000 individuals. All methods used an exhaustive search strategy for 2nd order interaction analysis.
* This computing time is estimated from the computing time in simulation data with 5000 SNPs.
All analysis are carried out on single core of a 3.16 GHz CPU with 4G memory on LINUX.

ISSN: 1755-8794