get_regulons: get_regulons

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

get_regulons

Description

Get regulons from the given loom file

Usage

get_regulons(
  loom,
  column.attr.name = "MotifRegulons",
  tf.as.name = TRUE,
  tf.sep = "_"
)

Arguments

loom	.loom file name
column.attr.name	Type of regulon to retrieve; Usually 'MotifRegulons' for motif-based regulons, or 'TrackRegulons' for track-based (e.g. ChIP-seq) regulons. (Might change according to the SCENIC/pySCENIC pipeline version and settings used).
tfAsName	Whether to return only the TF name (calls SCENIC::getTF()), or the regulon name as stored in the loom file.
tfSep	Character used as separator for the TF name and extra values stored in the regulon name. To be passed to SCENIC::getTF()

Value

The regulons as incidence matrix or list.

Examples

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

regulons <- get_regulons(loom)
head(regulons)

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