topicsRcisTarget: topicsRcisTarget

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

topicsRcisTarget

Description

Run RcisTarget in the binarized topics

Usage

topicsRcisTarget(
  object,
  genome,
  pathToDb,
  reduced_database = FALSE,
  nesThreshold = 3,
  rocthr = 0.005,
  maxRank = 20000,
  nCores = 1,
  ...
)

Arguments

object	Initialized cisTopic object, after the [e-mail] has been filled.
genome	Genome to which the data was aligned or liftovered (hg19, mm9, dm3 or dm6).
pathToDb	Path to the feather or parquet database to use. Note that this database has to match the genome used for mapping.
reduced_database	Whether a reduced version of the database (e.g. background database) is being used or not (by default, it is set to false).
nesThreshold	Minimum enrichment score that a motif should have to be included in the table
rocthr	ROC threshold for AUC calculation. For mouse and human, we recommend 0.005; for fly, 0.01.
maxRank	Number of regions consider for visualization. For mouse and human, we recommend 20000; for fly, 5000.
...	See RcisTarget

Value

Motif enrichment table is stored in [e-mail]

Examples

pathToDb <- "hg19-regions-1M-9species.all_regions.mc9nr.feather"
cisTopicObject <- topicRcisTarget(cisTopicObject, genome='hg19', pathToDb)
cisTopicObject

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.