CePa (version 0.8.1)

cepa.ora: Apply centrality-extended ORA on a single pathway

Description

Apply centrality-extended ORA on a single pathway

Usage

cepa.ora(dif, pc, bk = NULL, pathway = NULL, id = NULL, cen = "equal.weight",
    cen.name = if(is.function(cen)) deparse(substitute(cen))
    else if(mode(cen) == "name") deparse(cen)
    else cen,
    iter = 1000)

Value

A cepa class object

Arguments

dif

differential gene list

pc

a pathway.catalogue class object

bk

background gene list. If background gene list are not specified, use whole human genes

pathway

igraph object or edge list

id

identify which pathway in the catalogue

cen

centrality measuments, it can ce a string, function, or function that has been quoted

cen.name

centrality measurement names. This argument should be set if the cen is a function.

iter

number of simulations

Author

Zuguang Gu <[e-mail]>

Details

The function is always called by cepa.ora.all. But you can still use it if you realy want to analysis just one pathway under one centrality.

See Also

cepa.all

Examples

if (FALSE) {
data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI, id = 2)
}