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

In CePa: Centrality-Based Pathway Enrichment

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)

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

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.

Value

A cepa class object

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa.all

Examples

## Not run: 
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)

## End(Not run)

CePa documentation built on Oct. 8, 2024, 5:08 p.m.