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

In CePa: Centrality-Based Pathway Enrichment

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)

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