search for: find_overlapped_gene

Displaying 2 results from an estimated 2 matches for "find_overlapped_gene".

2016 Apr 05
2
Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges
...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, func...
2016 Apr 05
0
Is that an efficient way to find the overlapped , upstream and downstream rangess for a bunch of rangess
...ssuming 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 <- 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, func...