SetDatExpr: SetDatExpr

In smorabit/hdWGCNA: hdWGCNA

SetDatExpr

Description

This function specifies the gene expression matrix for co-expression network analysis.

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
group_name	A string containing a group present in the provided group.by column or in the Seurat Idents. A character vector can be provided to select multiple groups at a time.
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_group_name	A string containing the name of a group present in the multi.group.by column.
assay	The name of the assay in the Seurat object
slot	Slot to extract data for aggregation. Default = 'counts'. Slot is used with Seurat v4 instead of layer.
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.
features	A list of features to use to override the features that have been previously set.
wgcna_name	A string containing the name of the WGCNA slot in seurat_obj@misc. Default = NULL which retrieves the currently active WGCNA data

Details

SetDatExpr is a critical function of the hdWGCNA pipeline that determines the gene expession matrix that will be used for network analysis. We typically use this function to select a cell type or group of cell types for network analysis using the group.by parameter, but we provide additional parameters for further customization.

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.