dsyMatrix is not supported

[wanpinglee]

Dear authors,

Thank you so much for developing the tool. After I created aGDS, I encountered an error of "dsyMatrix is not supported" when performing STAARpipeline_Gene_Centric_Noncoding.r.

The complete error message is

Error in STAAR_O_SMMAT_sparse(G, Sigma_i, Sigma_iX, cov, residuals.phenotype,  :
  dsyMatrix is not supported.

Any idea how to fix the issue Thanks!

Best,

[xihaoli]

Hi Wan-ping,

Thanks for your question. Did you run your analysis and encounter this issue based on this dockerized R environment? Were you able to run individual analysis (Step 2) using STAARpipeline?

If not, could you please check and let us know your R version and sessionInfo()?

Please feel free to let me know if you have any additional questions.

Best, Xihao

[wanpinglee]

Hi Xihao,

Thanks so much for your help. No, I couldn't perform individual analysis either. The same error. My R session is shown below.

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/local/R4/lib/R/lib/libRblas.so
LAPACK: /usr/local/R4/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.2.0

Best, Wan-Ping

[xihaoli]

Hi Wan-Ping,

Thanks for your information. I wonder if this question is related to your later version of R. Could you please contact us via email to have a detailed discussion on your question?

Best, Xihao

[xihaoli]

Hi Wan-Ping,

Upon discussion, the issue is on the class (type) of Sigma_i from the null model object obj_nullmodel, which can be fixed by setting as(Sigma_i, "dsCMatrix").

Best, Xihao

[wanpinglee]

Thanks, Xihao.