aracne.networks-package: ARACNe-inferred gene networks from TCGA tumor datasets

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

Description

This package contains ARACNe-inferred networks from TCGA tumor datasets and functions to import new ones and export them into text form.

Details

Package:	aracne.networks
Type:	Package
License:	LGPL-3
LazyLoad:	yes

Author(s)

Federico M. Giorgi

Maintainer: Federico M. Giorgi <[e-mail]>

References

Giorgi,F.M. et al. (2016) ARACNe-AP: Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information. Bioinformatics 2016 Alvarez, M.J. et al. (2016) Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics 2016

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(regulonblca,file="",n=10)

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