Error in Fit STAAR null model step: asMethod(object) : matrix is not symmetric [1,2] about staarpipeline-tutorial HOT 6 CLOSED

Hi Xubing,

Thanks for letting me know. Could you please check (1) whether your sparse GRM is symmetric, and (2) whether the rowname/colname of your sparse GRM has all sample ids for your phenotype/covariate file.

Best,
Xihao

from staarpipeline-tutorial.

I have tested both info and got the "True":

unique(phenotype$sample.id %in% colnames(sgrm))
[1] TRUE
unique(colnames(sgrm) %in% phenotype$sample.id)
[1] TRUE
isSymmetric(sgrm)
Error in UseMethod("isSymmetric") :
no applicable method for 'isSymmetric' applied to an object of class "c('dsCMatrix', 'CsparseMatrix', 'dsparseMatrix', 'symmetricMatrix', 'dCsparseMatrix', 'dMatrix', 'sparseMatrix', 'compMatrix', 'Matrix', 'xMatrix', 'mMatrix', 'replValueSp')"
isSymmetric(as.matrix(sgrm))
[1] TRUE

from staarpipeline-tutorial.

Hi Xubing,

Could you please then check (1) whether fit_nullmodel() works if you set kins <- NULL (assuming samples are unrelated); and (2) whether your sample.id in phenotype data and rowname/colname of your sparse GRM have duplicates (if there are no duplicates, then the dimension of phenotype and sgrm should be exactly the same).

Best,
Xihao

from staarpipeline-tutorial.

The result of first command was:

obj_nullmodel <- fit_nullmodel(phenotype~age+sex+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10,
data=phenotype,kins=NULL,use_sparse=TRUE,kins_cutoff=0.022,id="sample.id",
family=gaussian(link="identity"),verbose=TRUE)
[1] "kins is NULL, fit generalized linear model."
It looks like code can run well without sgrm.

And the sgrm name was same to phenotype$sample.id, only different order between them:

length(colnames(sgrm))
[1] 641
length(phenotype$sample.id)
[1] 641

from staarpipeline-tutorial.

Hi Xihao,

I have tested another grm data which was generated by gcta tools and found that the script "STAARpipeline_Null_Model.r" runned successfully. I think maybe something error in old sgrm data which generated by FastSparseGRM.

In the end, thanks for your help.

Best
Xubing

from staarpipeline-tutorial.

Hi Xubing,

Thank you very much for the updates. I can confirm that STAARpipeline supports any valid (sparse) kinship/GRM as input, so you can safely proceed to the next steps.

I shall close this case for now. Please let me know if you have any other questions.

Best,
Xihao

from staarpipeline-tutorial.