getCounts: Get counts for the various data defined in a 'GRN' object

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Get counts for the various data defined in a GRN object

Description

Get counts for the various data defined in a GRN object.

Usage

getCounts(GRN, type, norm, permuted = 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 permuted and non-permuted data can be retrieved, while for peaks, only the non-permuted one (i.e., 0) can be retrieved.
norm	Logical. TRUE or FALSE. Should original (often raw, but this may not necessarily be the case) or normalized counts be returned?
permuted	TRUE or FALSE. Default FALSE. Should the permuted data be taken (TRUE) or the non-permuted, original one (FALSE)?

Value

Data frame of counts, with the type as indicated by the function parameters.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
counts.df = getCounts(GRN, type = "peaks", norm = TRUE, permuted = FALSE)

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.