getgobp: Create a table to record Gene Ontology Biological Process...
In qsz13/LANDD: Liquid Association for Network Dynamics Detection

Description Usage Arguments Value Examples

getgobp.community() generates a result file of ego gene X, significant GO terms of X, significant GO terms of genes within k steps of X, gene W, significant GO terms of W,

1 2	getgobp(graph, z.matrix, k = 2, n.cores = 4, cutoff = 1, community = TRUE, community.min = 5, term.limit = NA)

`graph`	The graph of gene network.
`z.matrix`	A matrix representing gene Z (selected scouting genes). Row names are the gene id in gene network.
`k`	An Integer giving the order of the network.
`n.cores`	The number of cores used for parallel computing.
`cutoff`	The threshold to find LA scouting genes.
`community`	Boolean. Whether compute the community of genes W or not.
`community.min`	Integer. The minimum number of genes numbers in a community.
`term.limit`	The maximum number of GO terms to list in a row of the table.

A table containing the IDs of scouting center genes W, over-represented GO terms by W, semantic similarity on the Gene Ontology system between the X ego network and all scouting center genes, average graph distance between gene X and W. W are grouped by network community. Each W community occupies a row.

## Not run: 
g <- graph.data.frame(as.matrix(read.table("HumanBinaryHQ_HINT.txt"))) 
getgobp(g,z,k=2,n.cores=4,cutoff=1,community=TRUE,community.min=5,term.limit = NA)
## End(Not run)