Comments (7)
Hi Jiefang,
looking at your command list, how did you perform "prediction" when fitting the model failed ( "first step" didn't complete")?
First you may confirm that the software is running as expected on your system using the examples provided.
Without access to the data its hard to provide guidance, I would try the following
- exclude covariates
- omit msize mrep
- reduce #SNPs
Cheers
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from bayesr.
Hi Jiefang,
I'm not familiar with the Biobank data, but bayesR only accepts 0,1,2 as genotypes, missing genotypes (NA) are allowed.
Your data should run within a day, without using the reduced update.
The *.hyp file provides current estimates of the parameters during the run of the program and can be used to monitor the computations. You could set -burnin to zero and -numit to a low number first and check the the &.hyp file.
Cheers
from bayesr.
from bayesr.
Hi Jiefang,
did you look at the output files generated for the run with "-numit 500"?
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from bayesr.
Hi Jiefang,
I seems that your files were not uploaded correctly, I can only see the name of the files but no content.
Before continuing the conversation you need to
A. Test that the software runs on your system as expected.
Did you run the examples that are provided with the software and do results agree with those in the example folders?
B. Make sure that your data is formatted as required by bayesR
Running only a few hunded iterations and looking at the output files can sometimes highlight issues with the input data or model specifications. Obviously, if you're not familiar with bayesR you don't always know what to look for. However, you could try to run bayesR using a subset of randomly selected SNPs (as suggested earlier), for example 50k, and compare the derived model with your expectations or results from previous analysis (e.g. GREML).
Cheers
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Related Issues (16)
- direction of effect estimates HOT 3
- Using -dfvara -3.0 HOT 1
- Printing additional information for all SNPs with -snpout argument HOT 3
- At line 1736 of file baymods.f90; Fortran runtime error: End of file
- How include random effects in the model HOT 5
- fam file HOT 2
- allele frequency HOT 3
- Format/Readme file issue HOT 1
- Missing phenotypic values in .fam file
- How do I run BayesR with large memory ? HOT 1
- How to adjust the proportion of SNPs with no additive effect ? HOT 3
- Could I input covariate file into BayesR model? HOT 5
- Shape parameter must be positive HOT 1
- Way to do a weighted phenotype analysis with BayesR?
- End-of-file during read error, discrepancy between PLINK .bim file and simulated .bim file? HOT 13
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