Question

How to loop over two files ...and calculate R^2 between SNPs

0

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anamaria ▴ 10

@anamaria-21976

Last seen 4.5 years ago

Hello,

I have two files (each has 300 lines)like this:

head 1g.txt
rs6792369
rs1414517
rs16857712
rs16857703
rs12239392
...

head 1n.txt
rs1042779
rs2360630
rs10753597
rs7549096
rs2343491
...

For each pair of rs# from those two files I can run this command in R

library(httr)
library(jsonlite)
library(xml2)

server <- "http://rest.ensembl.org"
ext <- "/ld/human/pairwise/rs6792369/rs1042779?population_name=1000GENOMES:phase_3:KHV"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)
head(fromJSON(toJSON(content(r))))
   d_prime       r2 variation1 variation2         population_name
 1 0.975513 0.951626  rs6792369  rs1042779 1000GENOMES:phase_3:KHV

What I would like to do is to do is to run this command for every SNP in one list (1g.txt) to each SNP in another list (1n.txt). Where SNP# is rs# and output every line of result in list.txt

The process is illustrated in the attachment. https://imgur.com/a/adpCskU

enter image description here

loops R • 972 views

ADD COMMENT • link updated 4.5 years ago by James W. MacDonald 67k • written 4.5 years ago by anamaria ▴ 10

score 1 · Answer 1 · 2020-06-22

1

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 days ago

United States

This isn't a Bioconductor question, since you aren't actually using any Bioconductor packages. For random questions about R you could try r-help@r-project.org. Or for random bioinformatics questions you can try biostars.org.

ADD COMMENT • link 4.5 years ago James W. MacDonald 67k

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Thanks! I was hoping that someone who did use bioconductor packages did encounter the same problem or if someone knows if there is a bioconductor packages that does this.

ADD REPLY • link 4.5 years ago anamaria ▴ 10

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All you are doing is repeated GET requests using the Ensembl API. I suppose somebody might have coded that up in a package, but I have no idea why one might do such a thing.

Do note that you are contemplating somewhere around 90,000 GET requests (300 * 300), which is an exceeding large number, and which if you don't space (timewise) accordingly will almost surely get your IP address banned by somebody at Ensembl. Put a different way, there has to be a different way to get these data that doesn't involve something as inefficient as what you propose.

Which is why I suggested Biostars.org, which is a better venue for questions like this. I would be surprised if Kevin Blighe or ATpoint haven't already answered something very similar over there already.

ADD REPLY • link 4.5 years ago James W. MacDonald 67k

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anamaria, have you not contacted Ensembl directly about this? They have a great support team.