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stephenslab / susieR

R package for "sum of single effects" regression.
https://stephenslab.github.io/susieR
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Confusion regarding the interpretation of output from confidence sets #130

Closed ZayedShahjahan373 closed 3 years ago

ZayedShahjahan373 commented 3 years ago

Hi,

I hope you are all doing well. I am working on a genetic fine-mapping project with simulated data and so far the susie function has performed as expected. I do have a question about the variable names returned by the 'sets' accessor. 'susie.mod$sets' returns a set of numbers that do not correspond to any of my variables in the matrix of SNVs; which are all labelled in this 'rsXXXX' style. Am I correct interpreting these numbers in the confidence set as the index positions of the columns in the SNV matrix?

Thank you, Zayed Shahjahan

gaow commented 3 years ago

@ZayedShahjahan373 yes those are indices of variables. You can configure it to match the genomic coordinate using pos. See ?susie_plot for details. But the function cannot label x-axis with rsID or any non-integer labels.

ZayedShahjahan373 commented 3 years ago

Thank you Dr. Wang. Much appreciated.