[R] Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges

[Michael Lawrence]

For the sake of prosterity, this question was asked and answered here:
https://support.bioconductor.org/p/80448

On Tue, Apr 5, 2016 at 10:27 AM, 何尧 <heyao at pku.edu.cn> wrote:
> I do have a bunch of genes ( nearly ~50000)  from the whole genome, which read in genomic ranges
>
> A range(gene) can be seem as an observation has three columns chromosome, start and end, like that
>
>        seqnames start end width strand
>
> gene1     chr1     1   5     5      +
>
> gene2     chr1    10  15     6      +
>
> gene3     chr1    12  17     6      +
>
> gene4     chr1    20  25     6      +
>
> gene5     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_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 <- subsetByOverlaps(curr_gene, other_genes)
>   return(list(n, gene))
> }
>
> system.time(lapply(1:100, function(idx)  find_overlapped_gene(idx, all_genes_gr)))
> However, for 100 genes, it use nearly ~8s by system.time().That means if I had 50000 genes, nearly one hour for just find overlapped gene.
>
> I am just wondering any algorithm or strategy to do that efficiently, perhaps 50000 genes in ~10min or even less
>
>
>
>
>
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>
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