Vince,
thanks a lot for the example streaming dbSNP over the internet and how
this is even faster than accessing the data locally. to me, this just
confirms that the current performance of the
SNPlocs.Hsapiens.dbSNP144.GRCh37 annotation package can be improved.
Hervé will look at it and hopef
Hi Robert,
Thanks for report this. I'll look into it.
H.
On 06/17/2016 09:53 AM, Robert Castelo wrote:
hi,
the performance of snpsByOverlaps() in terms of time and memory
consumption is quite poor and i wonder whether there is some bug in the
code. here's one example:
library(GenomicRanges)
I think you can get relevant information rapidly from the dbsnp vcf. You
would acquire
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz.tbi
and wrap in a TabixFile
> tf
class: TabixFile
hi,
the performance of snpsByOverlaps() in terms of time and memory
consumption is quite poor and i wonder whether there is some bug in the
code. here's one example:
library(GenomicRanges)
library(SNPlocs.Hsapiens.dbSNP144.GRCh37)
snps <- SNPlocs.Hsapiens.dbSNP144.GRCh37
gr <- GRanges(seqna
