runCisTopic: Run cisTopic

In plbaldoni/scChIPseqsim: Single-cell ChIP-seq Data Simulator Based on Pseudo-bulk Profiles

Description

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Usage

runCisTopic(
  sc,
  peaks = TRUE,
  returnSc = FALSE,
  clustering = "all",
  title = "cisTopic",
  seed = 2020,
  legend.title = "Cell Type",
  shape = NULL,
  shape.title = NULL
)

Arguments

sc	SingleCellExperiment data
peaks	either TRUE (call peaks), FALSE (do not call peaks), or a vector of logicals of length equal to nrow(sc) indicating the sequence of bins pertaining to peak regions
returnSc	whether or not to return the utilized SingleCellExperiment data and the vector of peaks
clustering	either 'all' (the default), 'none', 'hierarchical', 'louvain', or 'kmeans'
title	title of the plot
seed	the seed
legend.title	title of the legend
shape	shape of the umap plot
shape.title	title of the shape legend

Details

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Value

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Author(s)

Pedro L. Baldoni, [e-mail]

plbaldoni/scChIPseqsim documentation built on June 11, 2020, 7:41 p.m.