search for: gene4gene3gene5na

...cient way to find overlapped, upstream and downstream genes for each gene in the granges For example, assuming all_genes_gr is a ~50000 genes genomic range, the result I want like belows: gene_nameupstream_genedownstream_geneoverlapped_gene gene1NAgene2NA gene2gene1gene4gene3 gene3gene1gene4gene2 gene4gene3gene5NA Currently , the strategy I use is like that, library(GenomicRanges) find_overlapped_gene <- function(idx, all_genes_gr) { #cat(idx, "\n") curr_gene <- all_genes_gr[idx] other_genes <- all_genes_gr[-idx] n <- countOverlaps(curr_gene, other_genes) gene <- subset...