Get the number of genes for a GRN object.

Returns the number of genes (all or only non-filtered ones) from the provided RNA-seq data in the GRN object.

nGenes(GRN, filter = TRUE)

Arguments

GRN

Object of class GRN

filter

TRUE or FALSE. Default TRUE. Should genes marked as filtered be included in the count?

Value

Integer. Number of genes that are defined in the GRN object, either by excluding (filter = TRUE) or including (filter = FALSE) genes that are currently marked as filtered.

See also

nTFs

nPeaks

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 17:28:55] 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!
nGenes(GRN, filter = TRUE)
#> [1] 18822
nGenes(GRN, filter = FALSE)
#> [1] 35033