runGenie3: runGenie3

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

runGenie3

Description

Runs GENIE3 and formats the output

Usage

runGenie3(
  exprMat,
  scenicOptions,
  nParts = 10,
  resumePreviousRun = FALSE,
  allTFs = getDbTfs(scenicOptions),
  ...
)

Arguments

exprMat	Expression matrix
scenicOptions	Fields used: genie3wm, genie3ll (int)
nParts	Number of pieces to fragment the partial results into (to check progress or in case the job gets interrupted). Default: 10
resumePreviousRun	Reload partial results from a previous (interrupted) run and resume execution (default: FALSE).
allTFs	List of all TFs for the organism. The default value is all genes annotated as 'TFs' in the database, which is appropriate for most analyses. (This argument allows to modify this list, for example removing genes that might be wrongly annotated as TF in some organisms/database versions). Note that selecting only a small subset of TFs for the analysis will modify the output, and therefore the interpretation of the results!
...	Other arguments to pass to GENIE3 (e.g. ntrees=500)

Value

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

Examples

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)

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