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.