[BUG]: extract_instruments when set P1> 5e-08

[quanliustc]

Please make sure that this is a bug! If you have questions about how to use TwoSampleMR please use the Discussions function instead.

Describe the bug (required)

Provide a clear and concise description of what the bug is

Describe the current behaviour you observe (required)

Include code blocks with any error messages

Describe the behaviour you expect (required)

R code to reproduce the issue (required)

Please provide a minimal code snippet that will reproduce this issue

Contribute a solution (optional)

Please submit a pull request and/or briefly describe your proposed solution

System information

Please provide details of your operating system and R version

Additional context

Add any other context about the problem here

[quanliustc]

For this new version of TwoSampleMR_0.6.11,

bmi_exp_dat <- extract_instruments(outcomes = 'ieu-a-2',p1=5e-08)
length(bmi_exp_dat)
[1] 15
bmi_exp_dat <- extract_instruments(outcomes = 'ieu-a-2',p1=5e-07)
Error in if (out == "[]") { : argument is of length zero
Calls: extract_instruments ->

Ideally, higher p1 cutoff should get more SNPs, but here why this version without any SNP?

[lixiaodong1999]

I can only set p1 to 5e-08 now, 5e-06 or 5e-10 gives me an error

[kpCCCP]

但是当你将clump从true改为false的时候，是可以提取出来工具变量的，只不过数量很大

[CSSAlchemist]

我将p1设置为1e-05会出错.

[ldbldb]

但是当你将clump从true改为false的时候，是可以提取出来工具变量的，只不过数量很大

但是什么原因呢，后续单独进行clump吗？

[Haiyv-art]

这种错误之前版本出现过类似的情况吗？要多久可以解决呀？或者大家有没有什么办法可以解决呀？有没有小伙伴下载旧的版本0.6.9无法下载，出现下载错误的问题呀？下载0.6.10时出现的问题和0.6.11相同呀？

[Jyoti-Jittu]

I can only set p1 to 5e-08 now, 5e-06 or 5e-10 gives me an error

Facing the same issue! did you get any solution for this??

[Haiyv-art]

我现在只能将 p1 设置为 5e-08,5e-06 或 5e-10 给我一个错误

有解决的办法吗？

[CSSAlchemist]

我也是，只要p大于5e-08，就报错。还想请教下，如果想修改r2和kb，代码怎么改呢

…

---- 回复的原邮件 ---- | 发件人 | ***@***.***> | | 日期 | 2025年03月16日 13:47 | | 收件人 | ***@***.***> | | 抄送至 | ***@***.***>***@***.***> | | 主题 | Re: [MRCIEU/TwoSampleMR] [BUG]: extract_instruments when set P1> 5e-08 (Issue #602) | 我现在只能将 p1 设置为 5e-08,5e-06 或 5e-10 给我一个错误 有解决的办法吗？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***> Haiyv-art left a comment (MRCIEU/TwoSampleMR#602) 我现在只能将 p1 设置为 5e-08,5e-06 或 5e-10 给我一个错误 有解决的办法吗？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[Haiyv-art]

我也是，只要p大于5e-08，就报错。还想请教下，如果想修改r2和kb，代码怎么改呢
…

目前最新版本还是不行，可以用本地Clump试试。

[lixiaodong1999]

I can now extract SNPs, and it will be ready in a few days. You can try to retrieve the token again &nbsp; 乙酰水杨酸 ***@***.*** &nbsp;

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: ***@***.***&gt;; 发送时间: 2025年3月15日(星期六) 凌晨0:22 收件人: ***@***.***&gt;; 抄送: ***@***.***&gt;; ***@***.***&gt;; 主题: Re: [MRCIEU/TwoSampleMR] [BUG]: extract_instruments when set P1&gt; 5e-08 (Issue #602) I can only set p1 to 5e-08 now, 5e-06 or 5e-10 gives me an error Facing the same issue! did you get any solution for this?? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***&gt; Jyoti-Jittu left a comment (MRCIEU/TwoSampleMR#602) I can only set p1 to 5e-08 now, 5e-06 or 5e-10 gives me an error Facing the same issue! did you get any solution for this?? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***&gt;