SCENIC (version 1.1.2-01)

runGenie3: runGenie3

Description

Runs GENIE3 and formats the output

Usage

runGenie3(exprMat, scenicOptions, nParts = 10, ...)

Arguments

exprMat

Expression matrix

scenicOptions

Fields used: genie3wm, genie3ll (int)

...

Other arguments to pass to GENIE3 (e.g. ntrees=500)

Value

Writes the output as getIntName(scenicOptions, "genie3ll")

Examples

# NOT RUN {
library(SCENIC)
scenicOptions <- readRDS("int/scenicOptions.Rds")

loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom")
exprMat <- SCopeLoomR::get_dgem(SCopeLoomR::open_loom(loomPath))

genesKept <- loadInt(scenicOptions, "genesKept")
exprMatrix_filtered <- exprMat[genesKept,]
exprMat_filtered <- log2(exprMatrix_filtered+1) 

runGenie3(exprMat_filtered, scenicOptions)
# }