DCGL (version 2.1.2)

ASC: Identify DCGs (Differential Coexpressed Genes) based on 'Average Specific Connection'

Description

A method to pick out DCGs from microarray data based on 'Average Specific Connection' (ASC) (Choi et al. 2005).

Usage

ASC(exprs.1, exprs.2, link.method = c("qth", "rth", "percent")[1], cutoff)

Arguments

exprs.1

a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.

exprs.2

a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.

link.method

a character string indicating link filtration method, default is 'qth'.

cutoff

the cutoff of correlation-value, q-value or percent of links after link filtering. must be within [0,1].

Value

ASC

the Average Specific Connections of genes. This measure can be used to rank gene in terms of differential coexpression.

Details

ASC is the average value of the specific degree of the two conditions.

References

Choi, J.K., Yu, U., Yoo, O.J. and Kim, S. (2005) Differential coexpression analysis using microarray data and its application to human cancer, Bioinformatics, 21, 4348-4355.

Examples

data(exprs)
ASC(exprs[1:100,1:16],exprs[1:100,17:63],
	link.method = 'qth', cutoff=0.25)