A question about the function“MRlap”

[Shiyuan-228]

Hi，
When I use the function “MRlap”，there is always a problem：
Error in tidy_inputGWAS(exposure, need_chrpos, verbose) : 'HeaderGWAS' not found
OR
Error in h (simpleError (msg, call)):
An error occurred in evaluating the 'x' parameter when selecting a method for the't 'function: non integrated parameter
After referring to your suggestion, I have reinstalled "MRlap" package, but there is still a problem：Error in h (simpleError (msg, call)):
An error occurred in evaluating the 'x' parameter when selecting a method for the't 'function: non integrated parameter.
The data I used has already been uploaded to the image

Please advise.Thanks

[lcpilling]

Hi. I deleted my first response actually as I realise I was wrong: Ninon's function can take data frame as the input (so my suggestion would not fix the issue).

I've downloaded and had a quick look at the FinnGen GWAS and it looks fine. Thanks for providing your code to show how to renamed the columns etc. I do not know what would produce your error, You are using quite a strict p-value threshold of 5e-10 -- does your exposure definitely have SNPs below this? Is the heritability high enough to perform genetic correlation? These are just suggestions. Ninon may have the better answer as she is the expert here - I am merely a keen user of the package!

[Shiyuan-228]

Thank you for your suggestions！发自我的 iPhone在 2023年11月29日，20:16，Luke C. Pilling ***@***.***> 写道： Hi. I deleted my first response actually as I realise I was wrong: Ninon's function can take data frame as the input (so my suggestion would not fix the issue). I've downloaded and had a quick look at the FinnGen GWAS and it looks fine. Thanks for providing your code to show how to renamed the columns etc. I do not know what would produce your error, You are using quite a strict p-value threshold of 5e-10 -- does your exposure definitely have SNPs below this? Is the heritability high enough to perform genetic correlation? These are just suggestions. Ninon may have the better answer as she is the expert here - I am merely a keen user of the package! —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[xz-xxz]

@Shiyuan-228 Hi. Have you found a solution to this?

[yangyizhixiaomaomi]

@Shiyuan-228 Hi. Have you found a solution to this?

[lcpilling]

Hi @yangyizhixiaomaomi - I've not seen this error before when using it myself - do you have a reproducible example?

[lcpilling]

Are you providing the full GWAS summary statistics files? Looks like you might only be passing the instruments like for TwoSampleMR... MRlap need the whole GWAS file for both exposure and outcome.

It automatically prunes to find the lead SNPs to use as instruments, then uses LDSC to adjust for sample overlap.

If you want to specify the lead SNPs you want it to use, set do_pruning=FALSE and provide a vector of the RSIDs with user_SNPsToKeep=rsids

[yangyizhixiaomaomi]

@lcpilling thank you vary much! In fact,when I try to use the whole GWAS and delete unnecessary column,it works.Thank you