ld_clump error

[fabianacz]

I am trying to perform clumping using the 1000 genomes as reference dataset.

Here is my code

clump_data(
summaryset_orru_format,
clump_kb = 10000,
clump_r2 = 0.001,
clump_p1 = 1,
clump_p2 = 1,
pop = "EUR"
)

Error in api_query("ld/clump", query = list(rsid = dat[["rsid"]], pval = dat[["pval"]], :
The query to MR-Base exceeded 300 seconds and timed out. Please simplify the query

I tried another approach. Running local LD operations.

To get a path to plink you can do the following:

devtools::install_github("explodecomputer/genetics.binaRies")
plink <- genetics.binaRies::get_plink_binary()

To get the same LD reference dataset that is used by the API, you can download it directly from here:

http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz

and tried this

orru_clump <- ld_clump(
dplyr::tibble(rsid = summaryset_orru$rsid, pval = summaryset_orru$p, id = summaryset_orru$id),
plink_bin = plink,
bfile = "1kg.v3" #this is in the same directory of my R project
)

The outcome is

Clumping ebi-a-GCST90001942, 15141982 variants, using EUR population reference
PLINK v1.90b7 64-bit (16 Jan 2023) www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to C:\Users\corsfmdg\AppData\Local\Temp\Rtmp63D8xl\file393034026c62.log.
Options in effect:
--bfile 1kg.v3
--clump C:\Users\corsfmdg\AppData\Local\Temp\Rtmp63D8xl\file393034026c62
--clump-kb 10000
--clump-p1 0.99
--clump-r2 0.001
--out C:\Users\corsfmdg\AppData\Local\Temp\Rtmp63D8xl\file393034026c62

65210 MB RAM detected; reserving 32605 MB for main workspace.
Error: Failed to open 1kg.v3.bed.
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:\Users\corsfmdg\AppData\Local\Temp\Rtmp63D8xl\file393034026c62.clumped': No such file or directory

[zillurbmb51]

Unpack the.tgz file using tar zxvf then point the actual plink file which will be "EUR" or something

[fabianacz]

wow! thanks! Just adding to that -> it only worked for me when I extracted all the .bim .fam .bed files and added all to my working directory. Thanks!

[phyliciasy]

Hello. I have the same error report as you. I used tar to unzip it and put all the extracted files in my working position.

Do you have some suggestions? Thank you.