regulators: Interogate a coregnet object.

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

Description

Query the network for regulators of specific targets and targets of specific genes.

Usage

regulators(object, target = NULL, type = c("single", "coregulators"))
activators(object,target,type=c("single","coregulators"))
repressors(object,target,type=c("single","coregulators"))
targets(object,regulator=NULL,type=c("regulating","activating","repressing"))

Arguments

object	The network in the form of a coregnet object to query.
target	The target gene to query.
regulator	The regulator to query.
type	The type of regulation to obtain. Differs depending on the function used.

Value

For regulators if no target is given, returns integer vector with the number of targets for each regulators of the network. Given a non null vector, a vector of the union of the regulators of all the genes is returned. For activators and repressors the behavior is similar except that a target gene is needed. If type = "coregulators" then only the regulators, activators or repressors which are found to be co-regulators, co-activators or co-repressors of the target genes are given.

targets with no given regulator returns a character vector of all the target genes in the network. Specifying a vector of regulators will return a vector of the union of the targets of all these regulators. The type of regulation can be specified to return only the activated or repressed targets.

Author(s)

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

Examples

acts=apply(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)

regulators(co)
regulators(co,"A")
regulators(co,"A","coregulators")


activators(co,"A")
activators(co,"A","coregulators")

repressors(co,"A")
repressors(co,"A","coregulators")

targets(co)
targets(co,"a")
targets(co,"a","reg")
targets(co,"a","act")
targets(co,"a","rep")
targets(co,c("a","b"),"act")

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