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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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GENESIS null model not working #27

Closed whtop closed 1 year ago

whtop commented 1 year ago

When genesis null model is used in the code below, it returns: dsyMatrix not supported

results_individual_analysis <- Individual_Analysis(chr=chr,start_loc=start_loc,end_loc=end_loc, genofile=genofile,obj_nullmodel=obj_nullmodel,mac_cutoff=20, QC_label=QC_label,variant_type=variant_type, geno_missing_imputation=geno_missing_imputation)

xihaoli commented 1 year ago

Hi @whtop,

Thanks for reaching out. May I ask whether you have converted the genesis null mode to STAAR null model, using the genesis2staar_nullmodel() function? If the problem still persists, then the issue may be 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

whtop commented 1 year ago

Thank you!

This is exactly I do: as(Sigma_i, "dsCMatrix").

xihaoli commented 1 year ago

You're more than welcome. I shall close this issue, but let me know if you have any other questions.

Best, Xihao