Displaying 2 results from an estimated 2 matches for "subsetbyoverlaps".
2016 Apr 05
2
Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges
...ene5NA
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...
2016 Apr 05
0
Is that an efficient way to find the overlapped , upstream and downstream rangess for a bunch of rangess
...ne5 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, 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...