getgobp.all: Create a table to record Gene Ontology Biological Process...
In qsz13/LAS-release: Find LA-scouting genes
Description
Usage
Arguments
Value
Description
getgobp.all()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,
Usage
1
2
getgobp.all(graph, z.matrix, k = 2, n.cores = 4, cutoff = 1,
community.min = 5, term.limit = NA)
Arguments
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.min
An Integer confines the min gene numbers in community.
term.limit
The maximum number of GO terms to list in a row of the table.
Value
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.
qsz13/LAS-release documentation built on May 26, 2019, 12:35 p.m.
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Description Usage Arguments Value
Description
getgobp.all()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,
Usage
1 2 | getgobp.all(graph, z.matrix, k = 2, n.cores = 4, cutoff = 1,
community.min = 5, term.limit = NA)
|
Arguments
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.min |
An Integer confines the min gene numbers in community. |
term.limit |
The maximum number of GO terms to list in a row of the table. |
Value
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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