DRsort: Identify DRGs (Differential regulated Genes) and DRLs...

In DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

Description

The algorithm is to determine DRGs and DRLs from DCGs and DCLs by TF-to-target interaction knowledge.

Usage

DRsort(DCGs, DCLs, tf2target, expGenes)

Arguments

DCGs	a data frame or matrix for DCGs list.
DCLs	a data frame or matrix for DCLs list.
tf2target	a data frame or matrix for TF-to-target interaction pairs.
expGenes	a list for measured genes by array

Details

DRsort, is aimed to sift DCGs and DCLs according to regulation knowledge.

If a DCG is a TF, it is intuitively speculated that its related differential coexpression may be attributed to the change of its regulation relationships with its targets. So this type of DCGs are termed Differential Regulation Genes (DRGs). Besides if the upstream TFs of a DCG is identified, that DCG is possibly a differentially regulated target of an implicated regulator, and so such DCGs are also kept in the set of DRGs.

If a DCL happens to be a TF-to-target relation, we highlight this DCL because it is the direct attribution to differential regulation. This type of DCLs are termed TF2target_DCL. On the other hand, if there are one or more common TFs regulating the two genes of a DCL, we also give priority to this DCL because the change in the expression correlation of the two genes could be attributed to the disruption of their co-regulation by the common TFs. This type of DCLs are termed TF_bridged_DCLs. TF2target_DCL and TF_bridged_DCL, therefore, together form the set of Differentially Regulated Links (DRLs).

Value

A list with four components:

DCGs	Displaying all of Differentially Coexpressed Genes with annotated regulator information whether it is available.
DCLs	Displaying all of Differentially Coexpressed Links with annotated regulator information whether it is available.
DRGs	Differentially Regulated Genes by annotating regulator information.
DRLs	Differentially Regulated Links by annotating regulation pairs information
DCG2TF	Displaying DCGs and upstream TF of DCGs by pairs. It is another format of DRGs.
TF_bridged_DCL	Displaying another format of TF_bridged_DCL for the ease of following investigation.

Author(s)

Jing Yang, Hui Yu

Examples

data(exprs)
data(tf2target)
expGenes<-rownames(exprs[1:100,])

## Two differential co-expression analysis methods
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)

## Summarizing DCGs and DCLs from DCp and DCe derived results
DCsum.res<-DCsum(DCp.res,DCe.res,DCpcutoff=0.25,DCecutoff=0.25)

## Sorting out DRGs and DRLs from DCsum-outputted results
DRsort.res<-DRsort(DCsum.res$DCGs,DCsum.res$DCLs,tf2target,expGenes)
## or only sorting out DRGs and DRLs from DCe-outputted results
DRsort.res<-DRsort(DCe.res$DCGs,DCe.res$DCLs,tf2target,expGenes)


## DRGs list
DRsort.res$DRGs[1:3,]

## DRLs list
DRsort.res$DRLs[1:3,]

DCGL documentation built on May 1, 2019, 8:38 p.m.