All of your torrent of requests for help to have others do your work for
you are about genomics issues. Why aren't you posting on the Bioconductor
Help forum instead, where both the expertise and tools for such matters
exist? I would characterize your posts here as being largely inappropriate
for that reason.
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Fri, Jun 19, 2020 at 5:35 PM Ana Marija <sokovic.anamarija at
gmail.com>
wrote:
> Hi Rasmus,
>
> I got those SNPs from two GWAS-es which I run with different
> phenotypes and I would like to compare weather the top SNPs in both of
> them are in LD.
> So 1n.txt and 1g.txt are just top SNPs from those two GWAS-es.
> Unfortunately https://ldlink.nci.nih.gov/?tab=ldpair works for only
> two SNPs at the time and I need to do that for 300 pairs
>
> On Fri, Jun 19, 2020 at 6:42 PM Rasmus Liland <jral at posteo.no>
wrote:
> >
> > On 2020-06-19 14:34 -0500, Ana Marija wrote:
> > >
> > > I have two files (each has 300 lines)like this:
> >
> > The example looks quite similar to the R example in
> > https://rest.ensembl.org/documentation/info/ld_pairwise_get#ra
> > ...
> >
> > The question becomes: how did you query the
> > 600 variant names in 1g.txt and 1n.txt?
> >
> > curl
'https://rest.ensembl.org/ld/human/pairwise/rs6792369/rs1042779?'
> -H 'Content-type:application/json'
> >
> > shows the 26 population_names for the
> > rs6792369/rs1042779 combination ...
>
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> and provide commented, minimal, self-contained, reproducible code.
>
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