Summarize a GRN object to a named list for comparison with other GRN objects.

Note: This function, as all get functions from this package, does NOT return a GRN object.

getGRNSummary(GRN, silent = FALSE)

Arguments

GRN

Object of class GRN

silent

TRUE or FALSE. Default FALSE. Should the function be silent and print nothing?

Value

A named list summarizing the GRN object. This function does **NOT** return a GRN object, but instead a named lsit with the following elements:

  • data:

    • peaks, genes and TFs:

    • sharedSamples:

    • metadata:

  • parameters and config: GRN parameters and config information

  • connections: Connection summary for different connection types

    • TF_peak: TF-peak (number of connections for different FDR thresholds)

    • peak_genes: Peak-gene

    • TF_peak_gene: TF-peak-gene

  • network: Network-related summary, including the number of nodes, edges, communities and enrichment for both the TF-peak-gene and TF-gene network

    • TF_gene

    • TF_peak_gene

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> INFO [2023-08-16 17:28:40] 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!
summary.l = getGRNSummary(GRN)
#> INFO [2023-08-16 17:28:41]  Finished successfully. Execution time: 1.2 secs