print.cepa.all: print the cepa.all object

In CePa: Centrality-Based Pathway Enrichment

print the cepa.all object

Description

print the cepa.all object

Usage

## S3 method for class 'cepa.all'
print(x, ...)

Arguments

x	a cepa.all object
...	other arguments

Details

The function print the number of significant pathways under various centrality measures at p-value <= 0.01.

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.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)
res.ora

# 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)
res.gsa

## End(Not run)

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