Comments (7)
I doubt if my GRM matrix is causing this problem,so i make a new one by tools:gcta(I think users who asked questions before did this),but i still get this error in Iteration 9
Iteration 9 : Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'chol2inv': error in evaluating the argument 'x' in selecting a method for function 't': leading principal minor of order 2430 is not positive Calls: fit_nullmodel ... .Call -> .handleSimpleError -> h -> .handleSimpleError -> h In addition: Warning message: In .local(A, ...) : Cholmod warning 'not positive definite' at file ../Cholesky/t_cholmod_rowfac.c, line 430 Execution halted
from staarpipeline-tutorial.
Xihao,and i have an another question,Can phenotypes be logical?
If so, what changes will the model make?Can we directly set phenoadj.norm to 0 or 1?
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Hi @Jerryliu0024,
Thanks for reaching out. Let's address your questions one by one. Regarding your question on the null model, this post is most relevant. Can you check whether your GRM contains negative values? What are the minimum and maximum values of your generated GRM?
Best,
Xihao
from staarpipeline-tutorial.
Hi Xihao,thanks for your reply!! the minimum values of your generated GRM is 0,and maximum one is 0.556215,my GRM doesn't contain negative values.However,when i set the group.var
as NULL,the STAARpipeline_Null_Model_GENESIS.r
run well and obj_nullmodel_GENESIS.Rdata Successfully generated(but the running time is very short and there are no iterations),Is it related to my phenotype being a 0/1 variable? maybe it conflicts with group.var
from staarpipeline-tutorial.
Hi @Jerryliu0024,
Yes, if your phenotype is dichotomous (0/1), then the group
variable in STAARpipeline_Null_Model.r
and group.var
variable in STAARpipeline_Null_Model_GENESIS.r
should be left empty. Could you please try it again?
Best,
Xihao
from staarpipeline-tutorial.
Hi Xihao,I think this is indeed feasible!However ,I have questions about some parameters. For example,what's the meaning of input array id from batch file (Harvard FAS RC cluster)
,and when i running STAARpipeline_Gene_Centric_Coding.r,It reminds meError in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix!
from staarpipeline-tutorial.
Hi @Jerryliu0024,
Thanks for letting me know. It's great to hear you got the null model fitting step correctly. With your new questions,
(1) The example scripts in the tutorial indicate that you would need to submit a list of array jobs to perform the association analysis (and here we use Harvard FAS RC cluster as an example, which is based on slurm workload manager). Specifically, for STAARpipeline_Gene_Centric_Coding.r
, you would need to submit a total of 379 jobs, where an integer between 1 and 379 would be passed to arrayid
in each job. We also provide an accompanying shell script to facilitate this batch job submission process.
(2) I can confirm that this message is not an error, but rather indicates that the specific gene category is not a valid variant set (i.e. there is not enough variant annotated as plof
for a specific gene in your dataset). You may ignore this message safely.
Hope this helps.
Best,
Xihao
from staarpipeline-tutorial.
Related Issues (20)
- Error in seqGetData: Invalid dimension 'Start' and 'Length' HOT 5
- Null outputs from Sliding_Window() HOT 2
- Known_Loci_Pruning error HOT 2
- vcf to gds HOT 7
- #SNVs per case/control? HOT 1
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
- Dynamic Window dim(X) error HOT 3
- Can't annotate individual variant results HOT 2
- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
- Ukbiobank Agds files generation HOT 16
- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
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