runsusie error report: Error in (function (z, R, n, bhat, shat, var_y, z_ld_weight = 0, estimate_residual_variance = FALSE, : The dimension of R (0 x 0) does not agree with expected (500 x 500)

[phyliciasy]

I tidy the datainput and check the data structure based on the example dataset in this link: https://cran.r-project.org/web/packages/coloc/vignettes/a06_SuSiE.html

And my dataset (MY_LIST) passed the test: check_dataset(D4,req="LD")

And when I run: S1=runsusie(MY_LIST)

I have an error report: Error in (function (z, R, n, bhat, shat, var_y, z_ld_weight = 0, estimate_residual_variance = FALSE, : The dimension of R (0 x 0) does not agree with expected (500 x 500)

I do not know why it does not work. Please help me if possible. Thanks a lot.

[chr1swallace]

I suspect your rows/columns of your LD matrix are not named. I should make check_dataset() check for that

[phyliciasy]

Dear Dr. Wallace,

I have already solved it. It is because I name the snp list as "SNP". So the programming can not find the list named after "snp".

Thank you very much for replying me.=D

Best regards, Siyu

---

发件人: Chris Wallace @.> 发送时间: 2023年8月22日 19:00 收件人: chr1swallace/coloc @.> 抄送: @. @.>; Author @.***> 主题: Re: [chr1swallace/coloc] runsusie error report: Error in (function (z, R, n, bhat, shat, var_y, z_ld_weight = 0, estimate_residual_variance = FALSE, : The dimension of R (0 x 0) does not agree with expected (500 x 500) (Issue #126)

I suspect your rows/columns of your LD matrix are not named. I should make check_dataset() check for that

― Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/126#issuecomment-1687967753, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZIYCM7EFEVO364HXEH26BTXWSGMHANCNFSM6AAAAAA2TAOLE4. You are receiving this because you authored the thread.Message ID: @.***>