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What input should be provided to MetaSTAAR_merge? #5
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Hi @Hepit, Thanks for reaching out. If you are running a meta-analysis from real data, please feel free to contact us via email and we can share more details. Best, |
@xihaoli Thanks for the quick response ! Until I need to share data, I might keep the conversation here, if that is ok with you, just in case other people have the same questions I do. Understood about Currently, I have run Thanks a lot for your time and advice ! |
Hi @Hepit, Sure no problem. In this case, let me ask a quick question. For Best, |
Hi @xihaoli, I wasn't sure exactly what was wanted for that parameter, so the value I used was simply the median position of the variant set - but if there's a better way to go about it, I'm very happy to redo it. I took a look at the .rda cov file, and the matrix is rectangular. |
Hi @Hepit, Thanks for letting me know. MetaSTAAR has several general use cases: (1) generate the cov files for all possible variants across the genome, so that meta-analysis of any variant set can be default after the cov files are shared. In this case, the cov files are rectangular matrices and (2) generate the cov files for pre-defined variant sets, so that meta-analysis is performed for the underlying variant sets. In this case, the cov files are square matrices. Note that this is a special case of (1) by setting To clarify, Hope this helps. Best, |
Hi @xihaoli, Thanks, that does clarify a few things ! Still a few points of confusion though : In case (1), what does the "rectangle" (and its "longer arm") refer to? If I'm passing an entire chromosome to Also regarding case (1) : does this mean I can generate a single cov file for the whole genome, and define my variant sets of interest later? If so, when (in which function) do I define them? And should I still use Sorry for all these questions, and thanks a lot for your patience in answering them ! |
Hi @Hepit, The "rectangle" (and its "longer arm") refers to the illustration in Panel b of the Workflow Figure of the MetaSTAAR paper. The Yes, you can generate a single cov file for the whole genome, but it also depends on how large your dataset is. In practice, you can generate cov matrices with sufficiently large bandwidth ( Let me know your plan. Best, |
Hi @xihaoli, Thanks for the explanation, that clarifies so much ! I'd love to be added to the repo. Thanks again ! |
Hello,
I've generated sumstat & cov files for my two cohorts using
MetaSTAAR_worker_cov()
&MetaSTAAR_worker_sumstat()
, but I'm now unsure how to feed those files toMetaSTAAR_merge()
, which seems to be the next step in the pipeline. The main point of my confusion is thatMetaSTAAR_merge()
has no argument where I can specify the name under which I saved the sumstat & cov files; it only has arguments where I can specify the directory. (For the record, I'm using version 0.9.6.3 of the R package.)I also notice that the scripts that accompany your 2023 article don't seem to make use of
MetaSTAAR_merge()
at all, and rather use a customMetaSTAAR_merge_simulation()
function instead...Could you shed some light on how these functions are supposed to be used?
Thanks !
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