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overlapped_gene
2016 Apr 05
0
Is that an efficient way to find the overlapped , upstream and downstream rangess for a bunch of rangess
...e5 chr1 30 40 11 +
I just wondering is there an efficient 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_name upstream_gene downstream_gene overlapped_gene
gene1 NA gene2 NA
gene2 gene1 gene4 gene3
gene3 gene1 gene4 gene2
gene4 gene3 gene5 NA
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 <...