find_tar_genes: Create a gene list containing putative targets of ligand...

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Create a gene list containing putative targets of ligand activity.

Description

Create a gene list containing putative targets of ligand activity.

Usage

find_tar_genes(sobject, id1, id2, pval = 0.05, logfc = 0.25, spec = "human")

Arguments

sobject	A Seurat object containing all of the cells for analysis (required)
id1	The idents of the target cells (ligand-stimulated cells) (required)
id2	The idents of the unstimlated cells for comparison (required)
pval	The p-value to use as a cutoff for up-regulation of genes (default = 0.05)
logfc	The log2 fold-change to use as cutoff for up-regulation of genes (default = 0.25)
spec	The species of the gene set (default = "human", can also be "mouse")

Details

This gene list is needed as one of the inputs for the ligand-receptor analysis. This list should be generated to identify genes in the same target cells used in the findLigands function as the "targets" parameter. You do not have to use this particular function to generate that gene list, but you can use this function to do it.

Value

A list of target genes

Examples

## Not run: 
targets <- find_tar_genes(seurat_obj,
                          id1 = "d14",
                          id2 = "d35",
                          logfc = 0.25,
                          spec = "human")

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.