scOne: single-cell analysis of one sample

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

single-cell analysis of one sample

Description

A wrapper of the standard workflow of Seurat

Usage

scOne(
  object = NULL,
  nFeatures = 2000,
  nPC = 30,
  resolution = 0.5,
  perplexity = NULL
)

Arguments

object	Seurat object
nFeatures	Number of variable features to use
nPC	Number of principal components to use
resolution	Value of the resolution parameter
perplexity	Value of the perplexity parameter, set between 5 and 50

Value

Seurat object

References

Inspired by Stuart and Butler et al, Cell (2019)

Examples

Bystander <- scRead(sample_name = "Bystander", 
                    data_dir = system.file(
                      "extdata/H3N2_10X_matrix/Bystander/", 
                    package="Yeskit"), 
                    gene_column = 2, project_name = "H3N2", 
                    group_name = "Bystander", 
                    meta_file = system.file(
                      "extdata/H3N2_10X_matrix/Bystander/microbes.tsv", 
                      package="Yeskit")
                    )
Infected <- scRead(sample_name = "Infected", 
                    data_dir = system.file(
                      "extdata/H3N2_10X_matrix/Infected/", 
                    package="Yeskit"), 
                    gene_column = 2, project_name = "H3N2", 
                    group_name = "Infected", 
                    meta_file = system.file(
                      "extdata/H3N2_10X_matrix/Infected/microbes.tsv", 
                      package="Yeskit")
                    )
Integrated <- merge(Bystander, Infected)
Integrated <- scOne(object = Integrated, 
  nFeatures = 2000,
  nPC = 30,
  resolution = 0.7
)

ncrna/Yeskit documentation built on Oct. 27, 2023, 2:13 a.m.