FindCelltype: Identify cell types based on a user defined consensus markers

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

Description

Assign cell identities to clusters

Usage

FindCelltype(
  markers.file,
  consensus.file,
  object = NULL,
  output.dir,
  filename = NULL,
  save.rds = TRUE,
  label = TRUE,
  ...
)

Arguments

markers.file	Path to the markers file (FindAllMarkers() output)
consensus.file	Path to the consensus file
object	A Seurat object
output.dir	Path to the destination folder of saved files
filename	Character string to name the saved umap plots
save.rds	Save final Seurat object in RDS format (default set to True)
label	Boolean to display cluster labels on umap plots
...	Arguments passed to as.sparse

Value

A Seurat Object with cells identities assigned to clusters

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