RunTf: Create Dorothea Assay with TF activity computed using Viper

In Theob0t/scEasyPip: Automated Seurat Pipeline for scRNA-seq analysis

Description

Create Dorothea Assay with TF activity computed using Viper

Usage

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.