scIntegrate: scIntegrate

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

scIntegrate

Description

Integrate seurat objects into one

Usage

scIntegrate(
  object.list = NULL,
  object.names = NULL,
  nVariable = 2000,
  nPC = 30,
  resolution = 0.5,
  batch.rm = "harmony"
)

Arguments

object.list	A list of seurat objects
object.names	An array of seurat object names
nVariable	Number of features to select as top variable features
nPC	Number of PCs to use
resolution	Resolution parameter to set. Default resolution=0.5
batch.rm	Remove batch effect with 'seurat' or 'harmony'. Default batch.rm='harmony'

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 <- scIntegrate(object.list = list(Bystander, Infected), 
  object.names = c("Bystander", "Infected"),
  batch.rm = "harmony",
  resolution = 0.7
)

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