get_regulons_AUC: get_regulons_AUC

In aertslab/SCopeLoomR: Build .loom files (compatible with SCope) and extract data from .loom files.

get_regulons_AUC

Description

Get AUCell matrix from the given loom file

Usage

get_regulons_AUC(
  loom,
  column.attr.name = "MotifRegulonsAUC",
  rows = "regulons",
  columns = "cells"
)

Arguments

loom	.loom file name
column.attr.name	Type of regulon to retrieve; Usually 'MotifRegulonsAUC' for motif-based regulons, or 'TrackRegulonsAUC' for track-based (e.g. ChIP-seq) regulons. (Might change according to the SCENIC/pySCENIC pipeline version and settings used).
rows	Type of data stored as rows (only for informative purposes) Default: "regulons"
columns	Type of data stored as columns (only for informative purposes) Default: "cells"

Value

AUC matrix in the slot loom[["col_attrs"]][["RegulonsAUC"]][]. If AUCell is installed, it will be stored as aucellResults object.

Examples

loom_file_pathath <-  file.path(system.file('extdata', package='SCopeLoomR'), "example.loom")
loom <- open_loom(loomPath)

regulons_AUC <- get_regulons_AUC(loom)

aertslab/SCopeLoomR documentation built on April 19, 2022, 11:25 a.m.