Everything works fine for me with quote="":
> system.time(gwas
<-read.delim("gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv",
quote=""))
user system elapsed
4.435 0.052 4.487
> dim(gwas)
[1] 179364 38
> sessionInfo()
R version 4.0.0 Patched (2020-04-27 r78316)
Platform:
Thanks for checking this out. I am leaning towards readr::read_tsv which
is very explicit about
untoward content
Browse[2]>
debug: tab = readr::read_tsv(tf)
Browse[2]>
*Parsed with column specification:*
*cols(*
* .default = col_character(),*
* `DATE ADDED TO CATALOG` = **col_date(format
If you don't have lazy data on, you should be able to load the data by
using data(). Let us say you example data is called expData.
With lazy data
print(expData)
Without lazy data you need explicit loading
data(expData)
print(expData)
For the purpose of examples, there is also a
Dear Kasper,
Many thanks for your reply. Yes, I am using data() to load the data. However,
the problem is, when I checked my package using CMD Check, it threw me the
warning that I am using that data only in the example but not in code. I see
the disadvantages of LazyData, but I just want to
Hi,
You have to reset your commits before you can update your package again.
Please do something in the order of,
1) git reset --soft
2) Edit your DESCRIPTION file to fix the version number.
3) git add DESCRIPTION
4) git commit -m "Version bump"
5) git push origin master
6) git push
This seems really weird, and I don't think you should be using lazyData to
get a message to disappear. Is there a GitHub page where we can browse the
code and do you have the full output of R CMD check somewhere?
On Thu, Apr 30, 2020 at 9:05 AM Vinh Tran wrote:
> Dear Kasper,
>
> Many thanks
Please see forwarded message.
On Thu, Apr 30, 2020 at 11:55 AM Nitesh Turaga
wrote:
> Hi Hector,
>
> I've updated your email address on the BiocCredentials account. Please
> activate your account once again after this change with your new email
> address. All the settings should be saved as
Hi Hector,
I've updated your email address on the BiocCredentials account. Please
activate your account once again after this change with your new email
address. All the settings should be saved as they were before.
As soon as you activate your account you should have access to your
packages.
Hi,
Please hold off on making any further changes on your package for the
time being. It seems that there is an issue when you committed with the
merge conflicts.
I will reset your package, and you should make the changes again, with
the correct version number.
Please wait for a while so
Hi Lori
Just my two-cents: I would not miss UNIGENE.
I am using org.db's mostly to annotate primary gene identifiers (ENTERZID,
ENSEMBL) with
additional human readable information (SYMBOL, GENENAME), and to map between
different
primary identifiers. I mostly use, in decreasing order of
right, line 35265 of
http://www.ebi.ac.uk/gwas/api/search/downloads/alternative has an unclosed
quote in a field.
35265 2019-04-10 30804558Grove J 2019-02-25 Nat Genet
www.ncbi.nlm.nih.gov/pubmed/30804558I dentification of common
genetic risk variants for autism
This file trips up fread around record 170349, inconsistently ... I haven't
figured that out yet.
readLines, strsplit may be the ultimate solution.
On Thu, Apr 30, 2020 at 7:15 AM Vincent Carey
wrote:
> right, line 35265 of
> http://www.ebi.ac.uk/gwas/api/search/downloads/alternative has an
>
The EBI GWAS catalog is large -- now the download is over 100MB for 179K
associations. A "bug" in the
package was reported, so I acquired the file by hand.
> nn = read.delim("gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv",
sep="\t")
*Warning message:*
*In scan(file = file, what = what,
Hi Lori,
I agree with Michael. I for myself do not need the UNIGENE field. The
mot frequent columns that I use are:
ENTREZID, REFSEQ, ENSEMBL, SYMBOL, GENENAME, UNIPROT, gene_id and GO.
Best,
Tobias
Am 30.04.20 um 08:46 schrieb Stadler, Michael:
Hi Lori
Just my two-cents: I would not
I'd look instead at or around line 35264 for use of quotes, e.g., "3' DNA", and
change the argument read.delim(quote = "") (though I never get that right so
probably wrong again...). A comment character might also be a problem.
If you point to the location of the file I could investigate
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