Hi, thanks for getting back to me, it is just for my job :)
so I tried it: library(httr) library(jsonlite) library(xml2) library(SparkR, lib.loc = c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"))) sparkR.session(master = "local[*]", sparkConfig = list(spark.driver.memory = "2g")) server <- "http://rest.ensembl.org" 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")) write(r,file="list.txt",append=TRUE) } } and I got this error: Error in as.list.default(f1) : no method for coercing this S4 class to a vector Please advise On Fri, Jun 19, 2020 at 3:28 PM <cpolw...@chemo.org.uk> wrote: > > 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.