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 |
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.
1 2 3 4 | ## 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)
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