filterExpressedGenes: Filter and Sort Gene Expression List Based on Specified Genes...

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Filter and Sort Gene Expression List Based on Specified Genes and Expression Threshold

Description

This function takes a named list of gene expression values and a character vector of gene symbols. It identifies the intersection of gene symbols with names in the list, filters genes based on a specified expression threshold, and returns a character vector of genes that meet the criteria, sorted by expression in descending order.

Usage

filterExpressedGenes(
  genes,
  gene_list = all.genes,
  sort_by_expr = TRUE,
  threshold = 0.1
)

Arguments

genes	Character vector of gene symbols to search for in the gene list. Default: NULL.
gene_list	A named list of gene expression values where names are gene symbols, and values are expression levels. Default: all.genes
sort_by_expr	Logical value specifying whether to sort the resulting gene list by expression level.
threshold	Numeric value specifying the minimum expression level for filtering. Genes with expression values below this threshold will be excluded. Default: 0.1.

Value

A character vector of gene symbols that match the specified list, meet the expression threshold, and are sorted in descending order by expression level.

Examples

# Example usage:
gene_list <- list(ROBO2 = 0.9982406, CDH18 = 0.9981755, DCC = 0.9981755, AL589740.1 = 0.9981103)
genes <- c("ROBO2", "DCC", "AL589740.1", "UNKNOWN")
filterExpressedGenes(gene_list, genes, threshold = 0.9981)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.