This function sets up the expression matrix input for consensus WGCNA based on the metacell expression matrix, the full expression matrix, or a provided pseudobulk expression matrix.
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
- group_name
A string containing a group present in the provided group.by column or in the Seurat Idents.
- use_metacells
A logical determining if we use the metacells (TRUE) or the full expression matrix (FALSE)
- group.by
A string containing the name of a column in the Seurat object with cell groups (clusters, cell types, etc). If NULL (default), hdWGCNA uses the Seurat Idents as the group.
- multi.group.by
A string containing the name of a column in the Seurat object with groups for consensus WGCNA (dataset, sample, condition, etc)
- multi_groups
A character vecrtor containing the names of groups to select
- assay
The name of the assay in the Seurat object
- slot
The name of the slot in the Seurat object (counts, data)
- layer
Layer to extract data for aggregation. Default = 'counts'. Layer is used with Seurat v5 instead of slot.
- mat
A Matrix containing gene expression data. Supplying a matrix using this parameter ignores other options. This is almost exclusively used for pseudobulk analysis.
- wgcna_name
A string containing the name of the WGCNA slot in seurat_obj@misc. Default = NULL which retrieves the currently active WGCNA data