Load example GRN dataset

Loads an example GRN object with 6 TFs, ~61.000 peaks, ~19.000 genes, 259 filtered connections and pre-calculated enrichments. This function uses BiocFileCache if installed to cache the example object, which is considerably faster than re-downloading the file anew every time the function is executed. If not, the file is re-downloaded every time anew. Thus, to enable caching, you may install the package BiocFileCache.

loadExampleObject(
  forceDownload = FALSE,
  fileURL = "https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds"
)

Arguments

forceDownload

TRUE or FALSE. Default FALSE. Should the download be enforced even if the local cached file is already present?

fileURL

Character. Default https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds. URL to the GRN example object in rds format.

Value

An small example GRN object

Examples

GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> INFO [2023-08-16 17:28:52] Storing GRN@data$RNA$counts matrix as sparse matrix because fraction of 0s is > 0.1 (0.44)
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!