runSCENIC_1_coexNetwork2modules: runSCENIC_1_coexNetwork2modules

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

runSCENIC_1_coexNetwork2modules

Description

Step 1: Convert the output from GENIE3/GRNBoost to co-expression modules

Usage

runSCENIC_1_coexNetwork2modules(
  scenicOptions,
  weightThreshold = getSettings(scenicOptions, "modules/weightThreshold"),
  topThr = c(0.005),
  nTopTfs = c(5, 10, 50),
  nTopTargets = 50,
  aFun = topPerTf,
  corrThr = 0.03,
  linkList = NULL,
  corrMat = NULL,
  weightCol = "weight",
  verbose = getSettings(scenicOptions, "verbose")
)

Arguments

scenicOptions	Fields used: TODO
weightThreshold	Global weight threshold. Links with lower weight will be ignored in ALL modules.

Details

See the detailed vignette explaining the internal steps.

Value

The output is written in the folders 'int' and 'ouput'

Examples

runSCENIC_1_coexNetwork2modules(scenicOptions)

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.