write.regulon: Print a regulon object into a text file

In federicogiorgi/aracne.networks: ARACNe-inferred gene networks from TCGA tumor datasets

Description

This function will print the network into an output stream. Four columns will be printed: the Regulator id, the Target id, the Mode of Action (MoA, based on Spearman correlation that indicates the sign of the connection and ranges between -1 and +1), the Likelihood (essentially an edge weight that indicates how strong the mutual information for an edge is when compared to the maximum observed MI in the network, it ranges between 0 and 1).

Usage

write.regulon(
    regulon,
    file="",
    sep="\t",
    header=TRUE,
    n=Inf,
    regulator=NULL
)

Arguments

regulon	An object of class regulon
file	File name where the network will be printed
sep	String, a separator for the fields (default = "\t")
header	Logical. If a header should be printed. Default is TRUE
n	Numeric. How many interactions to print. Default is Inf
regulator	String. A particular regulator. Default is NULL

Value

Text output containing the network in tabular format.

Examples

### Create a random regulon with two hubs
# The first hub will have 100 targets
# The second hub will have 67 targets
regulon<-list()
regulon[["hub1"]]<-list(
    tfmode=setNames(runif(100,-1,1),paste0("target",sample(1:1000,100))),
    likelihood=runif(100,0,1)
)
regulon[["hub2"]]<-list(
    tfmode=setNames(runif(67,-1,1),paste0("target",sample(1:1000,67))),
    likelihood=runif(67,0,1)
)
class(regulon)<-"regulon"
write.regulon(regulon,file="network.txt")


### Print a the Prostate Adenocarcinoma (prad) network to standard output
# The gene ids are in Entrez format
data(regulonprad)
write.regulon(regulonprad,file="",n=10)

federicogiorgi/aracne.networks documentation built on May 16, 2019, 12:13 p.m.