DCe: To identify DCGs (Differentially-Coexpressed Genes) and DCLs (Differentially-Coexpressed Links)

Description

The algorithm first determines DCLs using a LFC model originially proposed for differential expression analysis, then determines DCGs with their sourrounding links enriched for DCLs.

Usage

DCe(exprs.1, exprs.2, method=Linkfilter.methods,cutoff, nbins=20, p=0.1,figname=c('LFC.s.jpeg','LFC.d.jpeg'))

Linkfilter.methods 
# c("rth", "qth", "percent")

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.

method

link filtering method

cutoff

cutoff used for link filtration, can be rth, qth, or percent depending on Linkfilter.method. must be within [0,1].

nbins

number of x bins for fitting y=a+(b/x).

the cutoff of q-value; must be within [0,1].

figname

names of figures of the LFC fitting results

Value

A list with four components:
DCGsDifferentially Coexpressed Genes
DCL.sameDifferentially Coexpressed Links of the same sign
DCL.diffDifferentially Coexpressed Links of different signs
DCL.switchedDifferentially Coexpressed Links of switched value

Details

DCe is based on the 'Limit Fold Change' or 'LFC' model, a robust statistical method originally proposed for selecting DEGs from microarray data (Mutch et al. 2002). With the analysis units changed from expression values to coexpression values, the LFC method with moderate adaption can be applied to screen for putative DCLs. DCGs with their surrounding links enriched for DCLs are determined through a binomial probability model.

References

Mutch, D.M., Berger, A., Mansourian, R., Rytz, A. and Roberts, M.A. (2002) The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data, BMC Bioinformatics, 3, 17. Yu H., Liu B-H., et al., Link-specific Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. Submitted. 2010

Examples

Run this code

data(dataC)
DCe(dataC[1:100,1:10],dataC[1:100,11:20],method = 'qth',cutoff=0.25,nbins=20,p=0.1)

Run the code above in your browser using DataLab