SCENIC (version 1.1.2-01)

exportsForArboreto: exportsForArboreto (alias: exportsForGRNBoost)

Description

Exports the TF list and expression matrix to text format to run GRNBoost (https://arboreto.readthedocs.io). Note that it is also possible to run the full pipeline of SCENIC in python. See https://pyscenic.readthedocs.io

Usage

exportsForArboreto(exprMat, scenicOptions, dir = "int")

Arguments

exprMat

Expression matrix

scenicOptions

Fields used: getDatasetInfo(scenicOptions, "org"), to select the annotation database.

dir

Output folder (by default 'int' in current working directory)

Value

Writes the output as text files.

Examples

# NOT RUN {
exportsForArboreto(exprMat, scenicOptions)
# }