Select Genes for Analysis

This function filters and selects transcription factors (TFs), target genes, and background genes from a Seurat object based on their expression in a minimum number of cells.

Usage

select.gene(seurat.obj, tfs = NULL, targets = NULL, bgs = NULL, min.cells = 20)

Arguments

seurat.obj

A Seurat object containing gene expression data.

tfs

A vector of transcription factor (TF) gene names. If NULL, all TFs in the gene.list$tfs will be considered. Default is NULL.

targets

A vector of target gene names. If NULL, all target genes in gene.list$targets will be considered. Default is NULL.

bgs

A vector of background gene names. If NULL, no additional background genes are considered. Default is NULL.

min.cells

An integer specifying the minimum number of cells in which a gene must be expressed to be included. Default is 20.

Value

A list containing:

tfs

Filtered TFs that meet the minimum cell expression criteria.

targets

Filtered target genes that meet the minimum cell expression criteria.

bgs

Filtered background genes, excluding any genes in tfs or targets.

genes

A unique set of all selected genes.

Details

The function first filters genes in the seurat.obj to retain only those expressed in more than min.cells cells. It then intersects the filtered gene set with provided or default lists of TFs, targets, and background genes.

See also

gr.graph

Examples

select.gene(seurat.obj)
#> Error: object 'seurat.obj' not found