SelectNetworkGenes: SelectNetworkGenes

In smorabit/hdWGCNA: hdWGCNA

SelectNetworkGenes

Description

Select genes that will be used for co-expression network analysis

Usage

SelectNetworkGenes(
  seurat_obj,
  gene_select = "variable",
  fraction = 0.05,
  group.by = NULL,
  gene_list = NULL,
  assay = NULL,
  wgcna_name = NULL
)

Arguments

seurat_obj	A Seurat object
fraction	A numeric that determines the minimum cells that a gene must be expressed in order to be included. For example, fraction = 0.05 means that 5% of cells must express a gene (count > 0) for it to be included.
gene_list	A character string of gene names, only used if type = "custom"
assay	Assay in seurat_obj to compute module eigengenes. Default is DefaultAssay(seurat_obj)
wgcna_name	name of the WGCNA experiment
type	How to select genes? Select "variable", "fraction", "all", or "custom".

Details

SelectNetworkGenes allows us to specify the genes that will be used for co-expression network analysis. This function is called by SetupForWGCNA. By default, the variable features in VariableFeatures(seurat_obj) are used. A custom gene list can also be used with the gene_list parameter and setting gene_select="custom".

We can also identify genes that are expressed above 0 in a certain proportion of the dataset by settting gene_select='fraction'. For example, by setting fraction=0.1 and group.by='seurat_clusters', this function will identify the set of genes that are expressed in 10% of cells in at least one of the clusters.

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