RunTf: Create Dorothea Assay with TF activity computed using Viper

Description Usage Arguments Value

View source: R/RunTfPipeline.R

Description

Create Dorothea Assay with TF activity computed using Viper

Usage

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RunTf(
  data.dir = NULL,
  object = NULL,
  species = "mouse",
  dorothea.confidence = c("A", "B", "C"),
  ...
)

Arguments

data.dir

Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name.

object

A Seurat object

species

Mouse or human

dorothea.confidence

Confidence levels of regulons

...

Arguments passed to as.sparse

Value

A processed Seurat Object along with visualization plots based on TF activity


Theob0t/scEasyPip documentation built on Dec. 18, 2021, 4:10 p.m.