NITRC Solar Eclipse Imaging Genetics tools Forum: open-discussion

More than 32000 individuals

Wouter Christiaansen — Thu, 07 Dec 2023 13:51:50 GMT

Hello,
I am trying to do a heritability analysis using data from over 100.000 individuals. I get an error that the maximum number of individuals is 32000, and I'd like to know if it is possible to run the software using a larger amount of data.  
Thank you!

RE: Couldn't install solar-9.0.0-Monterey for MAC

heng wang — Tue, 12 Apr 2022 7:27:33 GMT

Dear,

I really appreciated your kindly help! I've successfully re-download solar on my MAC. Thank you sooo much again!

RE: Couldn't install solar-9.0.0-Monterey for MAC

Brian Donohue — Thu, 03 Feb 2022 0:20:03 GMT

Heng,
If you came across another error involving a missing library named libgfortran then you should re-download the mac version one more time. Sorry for the inconvenience once again.

RE: Couldn't install solar-9.0.0-Monterey for MAC

Brian Donohue — Tue, 25 Jan 2022 13:17:34 GMT

Greetings,
Thanks for the feedback. I've updated the solar monterey release such that your error should no longer take place. Please let us know if you have anymore problems.

Couldn't install solar-9.0.0-Monterey for MAC

heng wang — Mon, 24 Jan 2022 8:00:35 GMT

Hello,
Recently, I'm so delighted to find that your team has released the new version of solar on MAC monterey. So, I couldn't wait to install it on my MAC. However, no matter how many times I tried, it always went something wrong with it. You could see it in the appendix file that I attached. I was wondering there may have something wrong with the "rlwrap" file. I'll be thankful for your kind help with my installation.

RE: Analysis of full-sibling pairs

heng wang — Fri, 19 Nov 2021 7:57:22 GMT

Dear Dr. Hatch,
Thank you so much for your reply! So, if I code the sibling pairs in the variable "MZtwins" in the pedigree file, then I can run the analysis of sibling-pairs. I was wondering that whether I understand it in a right way.

Thank you so much~
Best wisher!

RE: Analysis of full-sibling pairs

Kathryn Hatch — Mon, 15 Nov 2021 13:44:14 GMT

Hello Heng Wang,

Solar is capable of including full sibling pairs in your analysis. You simply need to code the sibling pairs in your pedigree with a value of 0.5. Thank you for reaching out and let us know if you have further questions.

Thanks!
The Solar Help Team

Analysis of full-sibling pairs

heng wang — Tue, 02 Nov 2021 8:27:03 GMT

Hello!

I'm now running an analysis of the full-sibling pairs, and I want to estimate the uni-heritability and bi-variate heritability of some phenotypes. I was wondering whether the SOLAR software is fitted for the full-sibling pairs estimation.

Thank you so much!

Best wishes!

RE: Unexpectedly high H2r

Kathryn Hatch — Fri, 09 Jul 2021 18:49:00 GMT

Hi Sam, Thank you for getting in touch.

The warning is simply triggered by high heritability value. It is to encourage you to do the sort of checking you have done.

High heritability should be taken in the context of the environmental factors including age and sex which have already been estimated and removed. Various other factors including unmodeled correlations may cause unexpectedly high heritability values, even 1.0 (not uncommon). Also don't forget to check the standard deviation of the heritability, as it might be difficult to estimate it very well with the present data. The most powerful transformation is inverse normalization such as:

[b]define itrait1 = inormal_trait1[/b]
[b]trait itrait1[/b]

I hope this helps. Please don't hesitate to contact us again for further clarification!

SOLAR-Eclipse Imaging Genetics Software Team

Unexpectedly high H2r

Sam Berry — Tue, 06 Jul 2021 14:04:26 GMT

Hello,

I am running some analyses on the HCP, testing for the heritability of mean diffusivity along along various white-matter tracts. For one of these tracts I get a H2r of 0.985 and a warning message 'Unexpectedly high heritabilities might result from numerical problems, especially if mztwins are present.' This is the case even after multiplying by the suggested factor or when I transform the data using the inverse log. I don't have this issue for the other data and when plotting them side-by-side I cannot see an obvious difference. I am not sure what numerical problems may be causing this, if it is indeed an error. Any help would be much appreciated. My model looks like this:
solarPolygenic(formula = inv_log_MeanMD_M1S1 ~ Age_in_Yrs +
Age_in_Yrs^2 + sex + Age_in_Yrs * sex + Age_in_Yrs^2 * sex +
MeanFD, data = df, covtest = TRUE, screen = TRUE)
Best wishes,
Sam
p.s Thank you for the software, I use it all the time!