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This function prepares the expression data for Consensus WGCNA analysis. It populates the multiExpr slot in the Seurat object, which contains a list of expression matrices (one for each consensus group, e.g., dataset, sample, condition).

Source: R/getters_and_setters.R
SetMultiExpr.Rd

The function operates in three modes:

  1. Internal Seurat/Metacell Mode (Default): Extracts expression data directly from the Seurat object (either single-cell or metacell data) based on group_name.

  2. Pseudobulk Mode (SummarizedExperiment): Extracts expression data from a provided SummarizedExperiment object (passed to mat). This is the recommended approach for pseudobulk consensus analysis.

  3. External Matrix Mode: Extracts expression data from a provided large matrix (passed to mat) where row names contain delimited group identifiers.

Usage

SetMultiExpr(
  seurat_obj,
  group_name,
  use_metacells = TRUE,
  group.by = NULL,
  multi.group.by = NULL,
  multi_groups = NULL,
  assay = NULL,
  slot = "data",
  layer = "data",
  mat = NULL,
  mat_group_delim = 3,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj

A Seurat object containing the hdWGCNA experiment.

group_name

A string containing the specific group to analyze (e.g., a specific cluster or cell type). This filters the data when using Internal Seurat/Metacell Mode.

use_metacells

Logical; if TRUE (default), use the metacell expression matrix stored in the hdWGCNA experiment. If FALSE, use the full single-cell expression matrix. Ignored if mat is provided.

group.by

A string containing the name of a column in the Seurat object with cell groups (clusters, cell types, etc). If NULL (default), uses Seurat Idents.

multi.group.by

A string containing the name of the column that defines the consensus groups (e.g., "dataset", "sample", "condition").

  • If using Seurat/Metacells, this must be a column in seurat_obj@meta.data.

  • If using Pseudobulk (SE), this must be a column in colData(mat).

multi_groups

A character vector specifying which groups from multi.group.by to include. If NULL, all unique groups are used.

assay

The name of the assay in the Seurat object (e.g., "RNA", "SCT").

slot

The name of the slot in the Seurat object (e.g., "counts", "data"). Used for Seurat v4 compatibility.

layer

The name of the layer in the Seurat object (e.g., "counts", "data") OR the name of the assay in the SummarizedExperiment (e.g., "VST", "counts") if mat is provided.

mat

A Matrix or SummarizedExperiment object containing gene expression data.

  • SummarizedExperiment: The function extracts the assay specified by layer and subsets columns based on multi.group.by in colData.

  • Matrix: The function assumes row names are delimited (e.g., "Cluster1:SampleA") and splits them using mat_group_delim.

mat_group_delim

Character; the delimiter used in the row names of mat if mat is a matrix (default is ":"). Ignored if mat is a SummarizedExperiment.

wgcna_name

A string containing the name of the WGCNA slot in seurat_obj@misc. Default = NULL, which retrieves the currently active WGCNA data.

...

Additional arguments passed to internal helper functions.

Value

A Seurat object with the multiExpr slot populated in the specified wgcna_name experiment.

Details

This function automatically aligns the genes in the provided data (mat or seurat_obj) with the genes selected for WGCNA (via SetupForWGCNA or GetWGCNAGenes). It also runs WGCNA::goodGenesMS to exclude genes with zero variance or excessive missingness across the consensus groups.