Displaying 2 results from an estimated 2 matches for "all_genes_gr".
2016 Apr 05
2
Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges
...ene2 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 <- functio...
2016 Apr 05
0
Is that an efficient way to find the overlapped , upstream and downstream rangess for a bunch of rangess
...e2 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_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...