R/TME-genes.R

In tanaylab/methylayer: Layered modeling of tumor methylation

#' Extract TME genes from methylation expression clustering
#' 
#' Extracts names of genes that were clustered together with canonical immune and CAF genes in the expression-methylation correlation matrix. This is used mostly for filtering those genes from additional analysis such as cis-regulation. 
#' 
#' @param em_list output of \code{em_cross_cor}
#' @param immune_gene name of canonical immune gene (default: CD3D). If NULL - only CAF genes would be returned.
#' @param caf_gene name of canonical immune gene (default: CAV1). If NULL - only immune genes would be returned.
#' 
#' @return vector with names of TME genes
#' 
#' @export
get_TME_genes <- function(em_list, immune_gene = "CD3D", caf_gene = "CAV1"){
	if (is.null(immune_gene)){
		regex <- caf_gene
	} else if (is.null(caf_gene)){
		if (is.null(immune_gene)){
			stop("Please provide at least one of immune_gene or caf_gene parameters")
		}
		regex <- immune_gene		
	} else {
		regex <- glue("({caf_gene})|({immune_gene})")
	}
	
	em_list$expr_clust %>%
        filter(grepl(regex, name)) %>%
        select(clust) %>%
        inner_join(em_list$expr_clust, by = "clust") %>%
        pull(name)
}