scstruc

The package for analysing the gene regulatory network based on the Bayesian network structure of single-cell transcriptomics data. The function works with SingleCellExperiment.

Installation

Using devtools:

devtools::install_github("noriakis/scstruc")

For using the CCDr algorithm in the latest R version, please install ccdrAlgorithm package from the following repository, which removes the || usage error.

devtools::install_github("noriakis/ccdrAlgorithm")

Examples

library(scran)
library(scstruc)
library(ggraph)
library(bnlearn)
sce <- mockSCE()
sce <- logNormCounts(sce)
included_genes <- sample(row.names(sce), 100)
gs <- scstruc(sce, included_genes, changeSymbol=FALSE)
#> Using default bnlearn algorithm: mmhc
plotNet(gs$net, gs$data, showText=FALSE)

Using the bootstrapping, the averaged network is obtained.

library(glmnet)
gs2 <- scstruc(sce, included_genes, algorithm="glmnet_BIC.boot",
               changeSymbol=FALSE, algorithm.args=list("R"=20))
#> Bootstrapping specified
plotAVN(gs2$net, sizeRange=c(1,3))