petal: Co-expression network modelling in R

BMC Systems Biology

Table 4 Empirical evaluation of petal’s runtime and memory requirement

Dimension of dataset	Metric	Runtime [hour]	Max memory [GB]
genes × measures
5,000×7	PE	1.35	1.0
5,000×7	SP	2.07	1.0
11,342×16	PE	2.62	7.0
11,342×16	SP	4.42	7.5
15,137×12	SP	9.20	13.5
15,137×16	SP	9.13	15.0
15,137×28	SP	9.15	13.0

Each row is a separate run on a server with 2.5 GHz processors, of which petal used one and 256 GB RAM. Datasets of different sizes were supplied to createSWSFnet FromFile to monitor the runtime and memory usage of the function. In two runs PE was specified as the metric to demonstrate its fast computing time compare to SP: createSWSFnetFromFile(~myData.txt~, ~PE~)

ISSN: 1752-0509