GREAT: GREAT

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

GREAT

Description

Run rGREAT in the binarized cisTopics

Usage

GREAT(
  object,
  genome = "hg19",
  liftOver = NULL,
  fold_enrichment = 2,
  geneHits = 1,
  sign = 0.05,
  request_interval = 20,
  ...
)

Arguments

object	Initialized cisTopic object, after [e-mail] has been filled.
genome	Genome to which the data was aligned (see rGREAT for options).
liftOver	GRangesList object containing the original coordinates (in the same format as [e-mail]) in the data set as slot names and the corresponding mapping regions as a GRanges object in the slot.
fold_enrichment	Minimum binomial fold enrichment to keep term.
geneHits	Minimum number of genes associated to keep term.
sign	Maximum adjusted p-value to keep term.
request_interval	Time interval for two requests.
...	See submitGreatJob from rGREAT

Details

This function works with regions annotated to hg19, hg18, mm10, mm9 and danRer7. For other genomes, a liftOver step to one of the available genomes is required.

Value

Non-empty GREAT results per topic are return as a list to [e-mail]

Examples

object <- GREAT(object, request_interval = 10)

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