Summarize DCGs and DCLs

Share:

Description

A algorithm to select synthetical DCGs and DCLs from the results of DCp and DCe.

Usage

1
DCsum(DCp.res, DCe.res, DCpcutoff = 0.25, DCecutoff = 0.25)

Arguments

DCp.res

a data frame generated by DCp, with rows as genes and columns as 'dC' score, 'links', 'p.value' and 'q.value' value.

DCe.res

a list generated by DCe, with two components which are DCGs and DCLs.

DCpcutoff

the cutoff of 'q.vaule' in DCp results; must be within [0,1]; If there is no 'q.value' value (when N=0), 'dC' will be sorted in decreasing order and retained the highest by 'DCpcutoff' percent.

DCecutoff

the cutoff of 'q' in DCGs components of DCe results; must be within [0,1].

Details

DCsum, short for Differentially Coexpression Summarization, summarizes 1) a set of DCGs, which is an intersection of DCp and DCe results; and 2) a set of DCLs which by definition must be connected with the DCGs. As a result, DCsum combines results from different coexpression analysis methods.

Value

A list with two components:

DCGs

Differentially Coexpressed Genes, combined two differential coexpression analysis

DCLs

Differentially Coexpressed Links, combined two differential coexpression analysis

Author(s)

Jing Yang, Hui Yu

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
data(exprs)
DCp.res<-DCp(exprs[1:100,1:16],exprs[1:100,17:63],
	link.method = 'qth',cutoff=0.25)
DCe.res<-DCe(exprs[1:100,1:16],exprs[1:100,17:63],
	link.method = 'qth',cutoff=0.25,nbins=20,p=0.1)
DCsum.res<-DCsum(DCp.res,DCe.res,DCpcutoff=0.25,DCecutoff=0.25)

## Differentially Coexpressed Genes after combination
DCsum.res$DCGs[1:3,]

## Differentially Coexpressed Links after combination
DCsum.res$DCLs[1:3,]