plotNull {CePa}R Documentation

Plot the null distribution of the pathway score

Description

Plot the null distribution of the pathway score

Usage

plotNull(x)

Arguments

x

a cepa object

Details

There are two figures in the plotting.

The function is always called through plot.cepa.all and plot.cepa.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

See Also

cepa, plot.cepa

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)
plotNull(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)
gsa = get.cepa(res.gsa, id = 5, cen = 3)
plotNull(gsa)

## End(Not run)

[Package CePa version 0.7.0 Index]