SCENIC (version 1.1.2-01)

runSCENIC_2_createRegulons: runSCENIC_2_createRegulons

Description

Step 2: RcisTarget (prune co-expression modules using TF-motif enrichment analysis)

Usage

runSCENIC_2_createRegulons(scenicOptions, minGenes = 20,
  coexMethod = NULL)

Arguments

scenicOptions

Fields used: TODO

minGenes

Minimum size of co-expression gene set (default: 20 genes)

coexMethod

Allows to select the method(s) used to generate the co-expression modules

Value

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

Details

See the detailed vignette explaining the internal steps.

Examples

# NOT RUN {
scenicOptions <- readRDS("int/scenicOptions.Rds")
# In case any settings need to be modified:
scenicOptions@settings$nCores <- 20
scenicOptions@inputDatasetInfo$org <- "mgi" 

runSCENIC_2_createRegulons(scenicOptions)
# }