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Set Expression Data (Standard WGCNA)

Source: R/getters_and_setters.R
SetDatExpr.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).

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

  3. External Matrix Mode: Sets the expression data from a provided matrix (passed to mat).

Usage

SetDatExpr(
  seurat_obj,
  group_name,
  use_metacells = TRUE,
  group.by = NULL,
  multi.group.by = NULL,
  multi_group_name = NULL,
  return_seurat = TRUE,
  assay = NULL,
  slot = "data",
  layer = "data",
  mat = NULL,
  features = NULL,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj

A Seurat object containing the hdWGCNA experiment.

group_name

A string containing the group to subset the data by (e.g., a specific cluster or cell type). Only used if pulling data from seurat_obj.

use_metacells

Logical; if TRUE (default), use the metacell expression matrix. 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 a column in the Seurat object with groups to subset further (e.g. dataset, sample). Only used if pulling data from seurat_obj.

multi_group_name

A string or character vector specifying which groups from multi.group.by to include.

return_seurat

Logical; if TRUE (default), returns the Seurat object with the datExpr slot populated. If FALSE, returns the data frame of expression data.

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 genes to match GetWGCNAGenes(seurat_obj).

  • Matrix: The function assumes columns are genes and rows are samples.

features

A character vector of genes to use. If NULL (default), uses the genes stored in the hdWGCNA experiment.

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 WGCNA::goodGenes.

Value

A Seurat object with the datExpr slot populated in the specified wgcna_name experiment, or a data frame if return_seurat = FALSE.

Details

This function sets up the expression matrix input for standard (non-consensus) WGCNA based on the metacell expression matrix, the full expression matrix, or a provided pseudobulk expression matrix.

This function automatically runs WGCNA::goodGenes to exclude genes with zero variance or excessive missingness. If mat is a SummarizedExperiment, the function automatically transposes the assay to the required (Samples x Genes) format.