CePa (version 0.8.1)

cepa.univariate: Apply centrality-extended GSA on a single pathway

Description

Apply centrality-extended GSA on a single pathway

Usage

cepa.univariate(mat, label, pc, 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, nlevel = "tvalue_abs", plevel = "mean",
    node.level.from.expr = NULL, node.level.t.value = NULL,
    r.node.level.from.expr = NULL)

Value

A cepa class object

Arguments

mat

expression matrix in which rows are genes and columns are samples

label

a sampleLabel object identify the design of the microarray experiment

pc

a pathway.catalogue object storing information of pathways

pathway

igraph object or edge list

id

identify the number of the pathway in the catalogue

cen

centrality measuments, it can ce a string, or function has been quote

cen.name

centrality measurement names

nlevel

node level transformation, should be one of "tvalue", "tvalue_sq", "tvalue_abs". Also self-defined functions are allowed, see cepa.univariate.all for detail.

plevel

pathway level transformation, should be one of "max", "min", "median", "sum", "mean", "rank". Also, self-defined functions are allowed, see cepa.univariate.all for detail.

node.level.from.expr

for simplicity of computing

node.level.t.value

for simplicity of computing

r.node.level.from.expr

for simplicity of computing

iter

number of simulations

Author

Zuguang Gu <[e-mail]>

Details

The function is always called by cepa.univariate.all. But you can still use it if you realy want to analysis just one pathway under one centrality.

Examples

if (FALSE) {

data(PID.db)

# 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.univariate(mat = eset, label = label, pc = PID.db$NCI, id = 2)
}