Get counts for the various data defined in a GRN object

Get counts for the various data defined in a GRN object. Note: This function, as all get functions from this package, does NOT return a GRN object.

getCounts(
  GRN,
  type,
  permuted = FALSE,
  asMatrix = FALSE,
  includeIDColumn = TRUE,
  includeFiltered = FALSE
)

Arguments

GRN

Object of class GRN

type

Character. Either peaks or rna. peaks corresponds to the counts for the open chromatin data, while rna refers to th RNA-seq counts. If set to rna, both real (foreground) and background data can be retrieved, while for peaks, only the real (i.e., the one with index 0) can be retrieved.

permuted

TRUE or FALSE. Default FALSE. Should the permuted data be taken (TRUE) or the non-permuted, original one (FALSE)?

asMatrix

Logical. TRUE or FALSE. Default FALSE. If set to FALSE, counts are returned as a data frame with or without an ID column (see includeIDColumn). If set to TRUE, counts are returned as a matrix with the ID column as row names.

includeIDColumn

Logical. TRUE or FALSE. Default TRUE. Only relevant if asMatrix = FALSE. If set to TRUE, an explicit ID column is returned (no row names). If set to FALSE, the IDs are in the row names instead.

includeFiltered

Logical. TRUE or FALSE. Default FALSE. If set to FALSE, genes or peaks marked as filtered (after running the function filterData) will not be returned. If set to TRUE, all elements are returned regardless of the currently active filter status.

Value

Data frame of counts, with the type as indicated by the function parameters. This function does **NOT** return a GRN object.

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
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
counts.df = getCounts(GRN, type = "peaks", permuted = FALSE)