getgobp: Create a table to record Gene Ontology Biological Process...

Description Usage Arguments Value Examples

View source: R/getgobp.R

Description

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,

Usage

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

Arguments

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.

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. W are grouped by network community. Each W community occupies a row.

Examples

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## 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)

LANDD documentation built on May 1, 2019, 8:12 p.m.