Executing this function is the very first step in the *GRaNIE* workflow. After its execution, data can be added to the object.

initializeGRN(objectMetadata = list(), outputFolder = ".", genomeAssembly)

## Arguments

List. Default list(). Optional (named) list with an arbitrary number of elements, all of which capture metadata for the object. Only atomic data types are allowed for each list element (see ?is.atomic for more help: logical, integer, numeric, complex, character, raw, and NULL), and this slot is not supposed to store real data. This is mainly used to distinguish GRN objects from one another by storing object-specific metadata along with the data.

outputFolder

Output folder, either absolute or relative to the current working directory. Default ".". Default output folder where all pipeline output will be put unless specified otherwise. We recommend specifying an absolute path. Note that for Windows-based systems, the path must be correctly specified with "/" as path separator.

genomeAssembly

Character. No default. The genome assembly of all data that to be used within this object. Currently, supported genomes are: hg19, hg38, mm9, mm10, rn6, rn7, dm6. If you need additional genomes, let us know. See function description for further information and notes.

## Value

Empty GRN object

## Examples

meta.l = list(name = "exampleName", date = "01.03.22")
GRN = initializeGRN(objectMetadata = meta.l, outputFolder = "output", genomeAssembly = "hg38")
#> INFO [2023-03-06 16:39:59] Empty GRN object created successfully. Type the object name (e.g., GRN) to retrieve summary information about it at any time.
#> INFO [2023-03-06 16:39:59]  Default output folder: /g/zaugg/carnold/Projects/GRN_packages/GRaNIE/docs/reference/output/
#> INFO [2023-03-06 16:39:59]  Genome assembly: hg38
#> INFO [2023-03-06 16:39:59] Finished successfully. Execution time: 0.1 secs