coregulators: Extract all co-regulators of a regulatory network.

In RemyNicolle/CoRegNet-bioc: CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Description

Based on the frequency and specificity of co-regulation, this functions extracts from a coregnet network all the cooperative regulators.

Usage

coregulators(object, maxcoreg = 2, verbose = TRUE, minCommonGenes = ifelse(maxcoreg == 2, 1, 10), adjustMethod = "fdr", alpha = 0.01)

Arguments

object	The coregnet object containing the co-regulatory network
maxcoreg	The maximum size of co-regulator sets to extract. The default is 2 to extract pairs of co-regulators
verbose	To output information during the extraction process. By default does not ouput anything except warnings.
minCommonGenes	The minimum number of commmon genes, co-regulated genes, to consider two regulators for further co-regulation analysis. Default is 1 for pairs and 10 for bigger sets.
adjustMethod	The p-value adjustment method to extract significant pairs of co-regulators. Default is FDR correction. Anything that is accepted by the p.adjust method is fine.
alpha	The threshold to consider a pair of co-regulator significant (after pvalue correction). Default is 1%

Value

For maxcoreg set to 2, a data.frame with pairs of regulators in the two first columns (Reg1 and Reg2), the Support (the portion of coregulated gene networks in which this pair is found), nGRN for the number of times the pair was found as cooperative regulators in the net, a p-value of a FisherTest testing the specificty of the shared targets and the adjusted pvalue of this test.

For maxcoreg higher than 2, a two column data.frame with the set of co-regulators (collapsed in one character seperated by a space) and the Support.

Author(s)

Remy Nicolle <remy.c.nicolle AT gmail.com>

See Also

regulators,hLICORN

Examples

acts=apply(rbind(rep("z",14),matrix(rep(letters[1:4],7),nrow=2)),2,paste,collapse=" ")[1:13]
reps=apply(matrix(rep(letters[5:8],7),nrow=2),2,paste,collapse=" ")[1:13]
grn=data.frame("Target"= LETTERS[1:26] ,"coact"=c(acts,reps),"corep"= c(reps,acts),"R2"=runif(26),stringsAsFactors=FALSE)
co=coregnet(grn)

coregulators(co)
coregulators(co,maxcoreg=3,minCommonGenes=3)

coregulators(co,adjustMethod="bonferroni")

coregulators(co,alpha=1)

RemyNicolle/CoRegNet-bioc documentation built on Dec. 18, 2021, 9:57 a.m.