Run_Integration: Run Integration Pipeline for Single-Cell Data

In eisascience/scCustFx: single-cell custom fxs Package

Run Integration Pipeline for Single-Cell Data

Description

This function performs multiple integration methods (Unintegrated, Harmony, RPCA, reference-based RPCA, LIGER) on a Seurat object and returns the integrated object with clustering and UMAP embeddings.

Usage

Run_Integration(
  SerObj,
  do.UnIntg = T,
  do.Harmony = T,
  useVarGenes = TRUE,
  nfeatures = 2000,
  spikeInGenes = NULL,
  dims = 1:15,
  harmony_res = 0.2,
  rpca_res = 0.2,
  rpca_ref_res = 0.4,
  reference = 1,
  LigerK = 20,
  nIteration = 30,
  Liger_res = 0.4
)

Arguments

SerObj	A Seurat object containing the single-cell RNA-seq data to be integrated.
do.UnIntg	Logical. If 'TRUE', performs the unintegrated analysis using PCA. Default is 'TRUE'.
do.Harmony	Logical. If 'TRUE', performs the Harmony-based integration. Default is 'TRUE'.
useVarGenes	Logical. If 'TRUE', uses variable genes for integration. Default is 'TRUE'.
nfeatures	Numeric. The number of variable features to select if 'useVarGenes' is 'TRUE'. Default is '2000'.
spikeInGenes	Character vector. A vector of spike-in genes to be added to the variable genes for semi-supervised integration. Default is 'NULL'.
dims	Numeric vector. Dimensions to use for PCA/UMAP and clustering (default is 1:15).
harmony_res	Numeric. The resolution for clustering after Harmony integration. Default is '0.2'.
rpca_res	Numeric. The resolution for clustering after RPCA integration. Default is '0.2'.
rpca_ref_res	Numeric. The resolution for clustering after reference-based RPCA integration. Default is '0.4'.
reference	Integer. Specifies which dataset to use as a reference for reference-based RPCA. Default is '1'.
LigerK	Integer. The number of factors for LIGER integration. Default is '20'.
nIteration	Integer. The number of iterations for LIGER's INMF algorithm. Default is '30'.
Liger_res	Numeric. The resolution for clustering after LIGER integration. Default is '0.4'.
do.rPCA	Logical. If 'TRUE', performs RPCA integration. Default is 'TRUE'.
do.rPCAref	Logical. If 'TRUE', performs reference-based RPCA integration. Default is 'TRUE'.
do.LIGER	Logical. If 'TRUE', performs LIGER-based integration. Default is 'TRUE'.

Value

The Seurat object ('SerObj') with added integration results, UMAP embeddings, and cluster assignments for each method run.

Examples

# Run integration with default settings
integrated_obj <- Run_Integration(SerObj)

# Run only Harmony and RPCA integration
integrated_obj <- Run_Integration(SerObj, do.UnIntg = FALSE, do.Harmony = TRUE, do.rPCA = TRUE, do.LIGER = FALSE)

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.