complete_restart: compares two given networks (original and augmented,...

In SDDE: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks

Description

This function is equivalent to the complete_network function, but it uses a fixed number of pathways to be investigated, which are divided in groups to allow restarting or better dispatching of tasks in a cluster environment.

Usage

	complete_restart(g1,g2,
					     taxnames,
					     resultfile='result.txt',
					     size=1000,
					     start=1,
					     end=0,
					     maxdistance=0,
					     maxtime=3600,
					     maxnode=0,
					     verbose=FALSE,
					     file='log.txt',
					     maxcores=1
					)

Arguments

g1	the original network X
g2	the augmented network Y with additional nodes (all the original nodes from X must be present in the augmented network Y)
taxnames	the taxon name of the nodes added to the original graph (default: we select all nodes that are not in g1)
resultfile	filename to which results are saved after each group (default='result.txt')
size	the number of paths to investigate at each iteration of the algorithm (default=1000)
start	the starting group of path lengths to investigate (default=1)
end	the ending group of path lengths to investigate (default=0 i.e. run until the end)
maxnode	the maximum number of augmented nodes in network Y to take into account (default=0, no maximum number of augmented nodes to take into account)
maxtime	the maximum search time per pathway (default=3600 seconds)
maxdistance	the maximum search distance to the added nodes in network Y (default=0, no maximum distance for augmented nodes to take into account)
verbose	flag to save into a file additionnal informations regarding the obtained paths (default=FALSE, the file name should be indicated)
file	filename to save the additionnal informations
maxcores	maximum number of cores to use (default=1, use 0 to use half of the total cores available )

Value

This function returns the number of paths of each category : Shortcuts, Detours, Dead ends, Equal paths and disconnected nodes.
If some of the augmented nodes are not visited because of the limits defined by maxnode, maxtime or maxdistance, a path can also be classified as 'Detour or Dead End'.

The format of the resultfile is as follow (tab-separated-value):
Columns:
1. Group number
2. Disconnected nodes
3. Shortcuts
4. Egals
5. Detours
6. Dead ends
7. Undefined detour or dead end*
8. Total path evaluated
9. User time (seconds)
10. System time (seconds)
11. Real time (seconds)
12. Disconnected total (up to this group)
13. Shortcut total (up to this group)
14. Egal total (up to this group)
15. Detour total (up to this group)
16. Dead end total (up to this group)
17. Undefined total (up to this group)
18. Total path evaluated (up to this group)
19. Total user time (up to this group)
20. Total system time (up to this group)
21. Total real time (up to this group)

Examples

## Searching the sample data (containing 11 original nodes and 3 augmented nodes)
data(Sample_1)
## Run from group number 1 to 2
complete_restart(g1,g2,size=5, start=1,end=2)

SDDE documentation built on May 1, 2019, 9:01 p.m.