Integrate Single-Cell Datasets

Unified interface for integrating heterogeneous single-cell datasets. Supports Seurat objects and matrices (via gene-wise aggregation and column concatenation).

Usage

SCIntegrate(
  ...,
  pipeline = "nsvpiectu",
  add.cell.ids = NULL,
  collapse = FALSE,
  merge.data = TRUE,
  merge.dr = FALSE,
  project = "Integrated Seurat"
)

SCIntegrate.data.frame(..., .quos = NULL)

SCIntegrate.Matrix(..., .quos = NULL)

SCIntegrate.Seurat(
  ...,
  pipeline = "nsvpiectu",
  add.cell.ids = NULL,
  collapse = FALSE,
  merge.data = TRUE,
  merge.dr = FALSE,
  project = "Integrated Seurat",
  .quos = NULL
)

Arguments

...

For matrix method: matrices to integrate, optionally named. For Seurat method: Seurat objects to integrate, followed by additional parameters passed to integration functions, Seurat objects and parameters are automatically filtered and passed to appropriate functions.

pipeline

Character string specifying processing steps for Seurat integration. Each letter represents a step: "n" = NormalizeData, "s" = ScaleData, "v" = FindVariableFeatures, "p" = RunPCA, "i" = IntegrateLayers, "e" = FindNeighbors (because n was used), "c" = FindClusters, "t" = RunTSNE, "u" = RunUMAP, "r" = SCTransform (because t was used),. Default: "nsvpiectu".

add.cell.ids

Character vector of prefixes for cell IDs when merging Seurat objects. Auto-inferred from argument names if not provided. (See Examples for details)

collapse

If TRUE, merge layers of the same name together; if FALSE, appends labels to the layer name

merge.data

Merge the data slots instead of just merging the counts (which requires renormalization); this is recommended if the same normalization approach was applied to all objects

merge.dr

Choose how to handle merging dimensional reductions: - “TRUE”: merge dimensional reductions with the same name across objects; dimensional reductions with different names are added as-is - “NA”: keep dimensional reductions from separate objects separate; will append the project name for duplicate reduction names - “FALSE”: do not add dimensional reductions

project

Project name for the Seurat object

.quos

Ignore it. Please do not pass any value

Value

• Matrix method: A matrix with all genes (union) and concatenated cells. Missing values filled with NA.

• Seurat method: Integrated Seurat object with processed layers according to pipeline.

Examples

if (FALSE) { # \dontrun{
# Matrix integration
mat1 <- matrix(rpois(100, 5), nrow = 20,
               dimnames = list(paste0("G", 1:20), paste0("C", 1:5)))
mat2 <- matrix(rpois(120, 6), nrow = 20,
               dimnames = list(paste0("G", 11:30), paste0("C", 1:6)))
integrated <- SCIntegrate(mat1, mat2)
dim(integrated)  # 20 genes × 11 cells

# Add customed prefixes to colnames
integrated <- SCIntegrate(A = mat1, B = mat2)
# > colnames(integrated)
# [1] "A_C1" "A_C2" "A_C3" "A_C4" "A_C5" "B_C1" "B_C2" "B_C3" "B_C4" "B_C5" "B_C6"

# Seurat integration with custom pipeline
seu1 <- CreateSeuratObject(mat1)
seu2 <- CreateSeuratObject(mat2)
integrated_seu <- SCIntegrate(seu1, seu2, pipeline = "nsfpi")
} # }