cepa.univariate {CePa}

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)

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

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.

Value

A cepa class object

Author(s)

Zuguang Gu <[e-mail]>

Examples

## Not run: 

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)

## End(Not run)