binarizecisTopics: Binarize cisTopic

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

Binarize cisTopic

Description

cisTopic binarization based on cisTopic scores

Usage

binarizecisTopics(
  object,
  method = "GammaFit",
  thrP = 0.99,
  plot = TRUE,
  cutoffs = NULL
)

Arguments

object	Initialized cisTopic object, after the [e-mail] has been filled with the cisTopic scores.
method	Method for the binarization, 'GammaFit' or 'Predefined'. If GammaFit, a gamma distribution will be fitted to the region scores distributions (a probability threshold must be provided); if threshold, a vector with the top number of regions to be taken per topic must be provided.
thrP	Probability threshold to use as cutoff on the probability distribution when using GammaFit as method.
plot	If TRUE, plots of the gamma fit per topic will be produced and a barplot with the number of regions taken per topic.
cutoffs	Vector (or scalar) with the top number of regions per topic to take per topic if Predefined is selected as method. If scalar, the same number of regions is taken per topic.

Value

A list with the selected regions per topic stored in [e-mail]

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