runSeurat: runSeurat

In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

runSeurat

Description

Perform usual Seurat step and cell type prediction.

Usage

runSeurat(
  expr,
  savePath,
  pc.use = 30,
  resolution = 0.8,
  clusterStashName = "default",
  bool.runDiffExpr = T,
  comb.method = NULL
)

Arguments

expr	A Seurat object return by prepareSeurat.
savePath	A path to save the results files. If NULL, the 'statPath' will be used instead.
pc.use	An integer number indicating the number of PCs to use as input features. The default is 30.
resolution	A float number used in function 'FindClusters' in Seurat. The default is 0.8.
clusterStashName	A character string used as the name of cluster identies. The default is "default".
bool.runDiffExpr	A logical value indicating whether to perform differential expressed analysis.
comb.method	The method used in combining samples. It worked only for multi-sample analysis.

Value

A list containing a Seurat object, differential expressed genes and annotation information for cells.

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.