Thank you so much as.character(r) indeed resolved the issue!
On Sat, Jun 20, 2020 at 3:47 AM Ivan Krylov wrote:
>
> On Fri, 19 Jun 2020 19:36:41 -0500
> Ana Marija wrote:
>
> > Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1),
> > "\n"), : argument 1 (type 'list') cannot be
On 2020-06-20 07:29 -0700, Bert Gunter wrote:
> On Fri, Jun 19, 2020 at 11:17 PM Rasmus Liland wrote:
> > On 2020-06-19 18:33 -0700, Bert Gunter wrote:
> > > Why aren't you posting on the
> > > Bioconductor Help forum instead
> >
> > Perhaps r-sig-genetics@ or r-sig-phylo@?
>
> genetics is not
genetics is not genomics. Nor are phylogenies. I still believe Bioc is the
right resource.
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
On Fri, 19 Jun 2020 19:36:41 -0500
Ana Marija wrote:
> Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1),
> "\n"), : argument 1 (type 'list') cannot be handled by 'cat'
It might be a good idea to try to solve problems like this yourself
instead of waiting for hours for someone to
Dear Bert,
On 2020-06-19 18:33 -0700, Bert Gunter wrote:
> All of your torrent of requests for help to
> have others do your work for you are about
> genomics issues.
I am a bioinformatician, I am supposed should
know all of these things, GWAS, Le ggplot,
etc. ...
> Why aren't you posting
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
unfortunately it complains again:
> f1 <- read_tsv("1g", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> f2 <- read_tsv("1n", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> for ( a in rownames(f1) ) {
+
+for ( b in rownames(f2)
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
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
Sorry - its been a long week!
there is a foreach package but I try to avoid extras
make your for statements:
for ( a in rownames(f1) ) {
# a will now be a row number rather than the value, so replace ' a ' in
the paste0 with: f1[ a, 1]
so
ext <- paste0( "/ld/human/pairwise/",
Dear other list readers,
On 2020-06-19 23:31 +0200, Rasmus Liland wrote:
> I have attached my rds here.
only Ana recieved this because of a Mailman
attachment policy, which also is why my
signature was bad ...
Best,
Rasmus
signature.asc
Description: PGP signature
I tried it:
> library(httr)
> library(jsonlite)
> library(xml2)
> library(readr)
> server <- "http://rest.ensembl.org;
> f1 <- read_tsv("1g", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> f2 <- read_tsv("1n", col_names=F)
Parsed with column specification:
cols(
Oh - read.text isn't in base! Not sure where is came from (my head
mostly!) You may have something that adds it but better to use
something that works. So try using:
library(readr)
f1 <- read_tsv("1g.txt", col.names=F)
This will give you a tibble with f1$X1 with the file in it
then loop
On 2020-06-19 16:07 -0500, Ana Marija wrote:
> HI Rasmus,
>
> I tried it:
>
> library(base)
>
> > r <- readRDS(paste0(population.name, ".rds"))
> Error in gzfile(file, "rb") : cannot open the connection
> In addition: Warning message:
> In gzfile(file, "rb") :
> cannot open compressed file
HI Rasmus,
I tried it:
library(base)
files <- c("1g.txt", "1n.txt")
files <- lapply(files, readLines)
server <- "http://rest.ensembl.org;
population.name <- "1000GENOMES:phase_3:KHV"
ext <- apply(expand.grid(files), 1, function(x) {
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 <-
On 2020-06-19 14:34 -0500, Ana Marija wrote:
>
> 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)
>
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,
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