so (untested) if you did something like
f1 <- read.text("1g.txt")
f2 <- read.text("1n.txt")
for ( a in as.list(f1) ) {
for ( b in as.list(f2) ) {
ext <- paste0( "/ld/human/pairwise/",
a,
"/",
b,
"?population_name=1000GENOMES:phase_3:KHV")
r <- GET(paste(server, ext, sep = ""),
content_type("application/json"))
# You presumably need to do something with 'r' at the
moment its over written by the next loop.. were
# you appending it to list.txt? Possibly its just a bit
of the R output you want.?
write(r,file="list.txt",append=TRUE)
}
}
Are we doing your PhD for you ;-) Do we get to share ;-)
On 2020-06-19 20:34, Ana Marija wrote:
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.
Please help,
Ana
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
