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Hi,
I have been trying to run fastGWA-mlm-binary and have been getting the error ' XtWX is not invertible'. I have adjusted for age and sex prior to the GWAS analysis and have only include PCs. Co…
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In the code I am writing, I am trying to preform stabilizing selection for plant height and heading date in wheat. I am able to successfully calculate a selection index which is returned as a matrix o…
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Hi, I want to convert a large VCF file (~3.5TB) to PLINK ped and map format files. But I got the log file as pasted below:
`Random number seed: 1707568963
773685 MB RAM detected; reserving 386842 …
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Hi,
I'm currently using regenie version 2.2.4 to analyze my data. However, it came up an error in step 1. It can't read my phenotype file. I've read past post for this kind of error, then I checked f…
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I received an unexpected error in version 2.2: ERROR: all individuals have missing/invalid values for phenotype 'X30620'.
it is a quantitative traits and 1000+ values for this trait. It should no…
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### Bug description
I have a covariate to include in the run_eggla_lmm() function. The following error occurs:
```r
Error in melt.data.table(data = data.table::as.data.table(data)[j = list(egg_id…
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Hi Steven,
Thank you for developing pypgx we use it quite a bit at our biobank . I am working on calling G6PD phenotypes for our participants.
I noticed all participants seem to be called "Indet…
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Hi!
Thank you for providing such a good software for MR!
I'm trying to run MRAPSS between multiple traits and one disease.
I noticed the warnings for top variants like below in the log files fo…
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### Bug description
I can see the various tables and images created from the archives function (line 152 run_eggla_lmm()) appear in the male and female directories that are created (line 157). howeve…
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Hello, I'm trying to run fastGWA and I have a few questions:
1. Does it estimate h2g after regressing out covariates in the fastGWA-REML step? Would the heritability be soaked by PCs etc.? What I s…