runClustering: Perform clustering on Seurat object

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

Description

Perform clustering on Seurat object

Usage

runClustering(
  object,
  output.dir,
  ndims,
  dims,
  resolution,
  no.plot,
  sctransform
)

Arguments

object	A Seurat object
output.dir	Path to the destination folder of saved files
ndims	Number of dimensions to plot standard deviation for
dims	Which dimensions to use as input features, used only if features is NULL
resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
no.plot	If set, run the pipeline without saving the plots
sctransform	If set, use SCTransform normalization

Value

A Seurat object with cells clustered and some cluster visualizations

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