CePa (version 0.8.1)

p.table: Table of p-values of pathways

Description

Table of p-values of pathways

Usage

p.table(x, adj.method = NA, cutoff = ifelse(adj.method == "none", 0.01, 0.05))

Value

A data matrix where rows are pathways and columns are centralities.

Arguments

x

a cepa.all object

adj.method

methods in p.adjust, available methods are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"

cutoff

cutoff for significance

Author

Zuguang Gu <[e-mail]>

Details

Since the p-values for each pathway are calculated for several centralities, the whole p-values are represented as a table.

Also it can extract significant pathways only.

See Also

cepa.all

Examples

if (FALSE) {
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)
p.table(res.ora)
p.table(res.ora, adj.method = "BH")

# 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)
p.table(res.gsa)
}