get.cepa: get single cepa object from cepa.all object

In CePa: Centrality-Based Pathway Enrichment

get single cepa object from cepa.all object

Description

get single cepa object from cepa.all object

Usage

get.cepa(x, id = NULL, cen = 1)

Arguments

x	a cepa.all object
id	index or the name of the pathway
cen	index or the name of the centrality

Details

The 'cepa.all object contains the result for pathways under several centrality measurements. In cepa.all object, each pathway under a specific centrality is a single cepa object. The get.cepa function is used to get the cepa object from the cepa.all object.

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa, cepa.all

Examples

## Not run: 
data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)
ora = get.cepa(res.ora, id = 5, cen = 3)

# GSA extension
# P53_symbol.gct and P53_cls can be downloaded from
# http://mcube.nju.edu.cn/jwang/lab/soft/cepa/
eset = read.gct("P53_symbol.gct")
label = read.cls("P53.cls", treatment="MUT", control="WT")
# will spend about 45 min
res.gsa = cepa.all(mat = eset, label = label, pc = PID.db$NCI)
gsa = get.cepa(res.gsa, id = 5, cen = 3)

## End(Not run)

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