# ISG Workshop 2022 **URL:** https://isgw-forum.colorado.edu/c/isg-workshops-2022/11.md [Latest](https://isgw-forum.colorado.edu/latest.md) · [Categories](https://isgw-forum.colorado.edu/categories.md) · [Tags](https://isgw-forum.colorado.edu/tags.md) --- ## [About the ISG Workshop 2022 category](https://isgw-forum.colorado.edu/t/about-the-isg-workshop-2022-category/31)
**Author:** [@JML](https://isgw-forum.colorado.edu/u/JML)\ **Replies:** 0
Discussion of course material, daily lectures, and practicals --- ## [Nuanced use of PCs with GRMs](https://isgw-forum.colorado.edu/t/nuanced-use-of-pcs-with-grms/816)
**Author:** [@rbhowmic](https://isgw-forum.colorado.edu/u/rbhowmic)\ **Replies:** 0\ **Last updated:** [June 5, 2026, 2:04pm UTC](https://isgw-forum.colorado.edu/t/nuanced-use-of-pcs-with-grms/816 "2026-06-05T14:04:43Z")
We had a helpful discussion on the selection of covariates for GWAS analysis on Day4. While GRMs capture genetic relatedness, including PCs is also recommended to account for overall genotype similarity across population… --- ## [Requirements for twin analysis](https://isgw-forum.colorado.edu/t/requirements-for-twin-analysis/531)
**Author:** [@handeezgia](https://isgw-forum.colorado.edu/u/handeezgia)\ **Replies:** 2\ **Last updated:** [March 20, 2023, 9:44am UTC](https://isgw-forum.colorado.edu/t/requirements-for-twin-analysis/531 "2023-03-20T09:44:33Z")
Hi! I am trying to run twin model by using my own dataset. However, the MZs correlations are not twice the size of Dz correlations. In this case, can I use twin modelling in my dataset? Example : Mz correlation for tra… --- ## [HWE and selection](https://isgw-forum.colorado.edu/t/hwe-and-selection/484)
**Author:** [@cpr2139](https://isgw-forum.colorado.edu/u/cpr2139)\ **Replies:** 2\ **Last updated:** [March 6, 2023, 10:33pm UTC](https://isgw-forum.colorado.edu/t/hwe-and-selection/484 "2023-03-06T22:33:34Z")
Is it ever possible that deviations from HWE are actually not a problem, but a signal of selection occurring for or against a phenotype? My intuition is that the kinds of timescales required to generate such a deviation … --- ## [Power to Detect E and r(e)](https://isgw-forum.colorado.edu/t/power-to-detect-e-and-r-e/385)
**Author:** [@ColinFreilich](https://isgw-forum.colorado.edu/u/ColinFreilich)\ **Replies:** 2\ **Last updated:** [September 15, 2022, 5:28pm UTC](https://isgw-forum.colorado.edu/t/power-to-detect-e-and-r-e/385 "2022-09-15T17:28:45Z")
Hi all, I was wondering if anyone had resources for detecting unique environmental variance and unique environmental correlations. I think I understand why this is not possible using the weighted noncentrality parameter… --- ## [Multiple imputation with mice of twin datasets](https://isgw-forum.colorado.edu/t/multiple-imputation-with-mice-of-twin-datasets/381)
**Author:** [@sinziana.oncioiu](https://isgw-forum.colorado.edu/u/sinziana.oncioiu)\ **Replies:** 2\ **Last updated:** [July 28, 2022, 12:09pm UTC](https://isgw-forum.colorado.edu/t/multiple-imputation-with-mice-of-twin-datasets/381 "2022-07-28T12:09:07Z")
Hi, I am struggling with imputation of covariates in a twin dataset. I am using co-twin design (generalised estimating equations) to estimate the within- and between-family effects. For the outcome and exposure, I am us… --- ## [Standardization](https://isgw-forum.colorado.edu/t/standardization/372)
**Author:** [@hallerl1](https://isgw-forum.colorado.edu/u/hallerl1)\ **Replies:** 2\ **Last updated:** [July 15, 2022, 12:56am UTC](https://isgw-forum.colorado.edu/t/standardization/372 "2022-07-15T00:56:00Z")
Hi, I was wondering if there is a preference with regards to standardizing a phenotypic (continuous) variable when running a classical twin design and sex-limited twin design? Does the variable need to be standardized t… --- ## [Installation problems with GCTA in mac system](https://isgw-forum.colorado.edu/t/installation-problems-with-gcta-in-mac-system/380)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 1\ **Last updated:** [July 11, 2022, 9:20pm UTC](https://isgw-forum.colorado.edu/t/installation-problems-with-gcta-in-mac-system/380 "2022-07-11T21:20:58Z")
Hi, I don’t know whether this is a good place to ask about the question of the installation of GCTA. I have tried to run GCTA and LDSC on my own laptop which is macbook with OS system for the practical. However, it seem… --- ## [Running Script Without Covariate](https://isgw-forum.colorado.edu/t/running-script-without-covariate/379)
**Author:** [@hallerl1](https://isgw-forum.colorado.edu/u/hallerl1)\ **Replies:** 1\ **Last updated:** [July 11, 2022, 8:58pm UTC](https://isgw-forum.colorado.edu/t/running-script-without-covariate/379 "2022-07-11T20:58:30Z")
Hi, I was wondering how to best alter the script for the sex-limitation models if not including a covariate? As far as I can tell, I would not run covVars, defAge, or pathB. This means other lines of the script need to… --- ## [OpenMx on ARM CPU](https://isgw-forum.colorado.edu/t/openmx-on-arm-cpu/375)
**Author:** [@Giaco](https://isgw-forum.colorado.edu/u/Giaco)\ **Replies:** 2\ **Last updated:** [July 3, 2022, 4:45pm UTC](https://isgw-forum.colorado.edu/t/openmx-on-arm-cpu/375 "2022-07-03T16:45:26Z")
Hi all, quick question on using OpenMx on ARM CPU: which optimizer do you recommend to use, since NPSOL is not supported on such architecture Installing OpenMx | OpenMx ? Will try to tag @michael.neale, but please let … --- ## [Creating a variable for a phenotype in each twin](https://isgw-forum.colorado.edu/t/creating-a-variable-for-a-phenotype-in-each-twin/373)
**Author:** [@pascaleac](https://isgw-forum.colorado.edu/u/pascaleac)\ **Replies:** 1\ **Last updated:** [June 28, 2022, 12:26am UTC](https://isgw-forum.colorado.edu/t/creating-a-variable-for-a-phenotype-in-each-twin/373 "2022-06-28T00:26:23Z")
I was reviewing the Day 1 script and noticed the variables, WT\_T1, and WT\_T2 describing the weight for twin 1 and twin 2. I am currently working with a dataset that does not include pre-calculated T1 and T2 variables fo… --- ## [Asking questions about heritability](https://isgw-forum.colorado.edu/t/asking-questions-about-heritability/374)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 2\ **Last updated:** [June 26, 2022, 10:53am UTC](https://isgw-forum.colorado.edu/t/asking-questions-about-heritability/374 "2022-06-26T10:53:32Z")
Hi, I would like to ask one simiple question but seems confusing me a little bit about heritability. Why is heritability is H2 but not H? I have tried to search for answers from Internet, but there seems to be no quick … --- ## [Asing several questions related to the lectures on day 6](https://isgw-forum.colorado.edu/t/asing-several-questions-related-to-the-lectures-on-day-6/351)
**Author:** [@xueyingqin](https://isgw-forum.colorado.edu/u/xueyingqin)\ **Replies:** 2\ **Last updated:** [June 24, 2022, 5:59am UTC](https://isgw-forum.colorado.edu/t/asing-several-questions-related-to-the-lectures-on-day-6/351 "2022-06-24T05:59:03Z")
Hi, I would like to ask several questions related to the lectures on day 6. For the lecture " \[Biometrical Age-Based Latent Growth Curve Modeling\].", there is one point in the last slide which stated that “REALLY IMP… --- ## [Violating Assumptions of Equal Means and Variances](https://isgw-forum.colorado.edu/t/violating-assumptions-of-equal-means-and-variances/343)
**Author:** [@hallerl1](https://isgw-forum.colorado.edu/u/hallerl1)\ **Replies:** 3\ **Last updated:** [June 23, 2022, 12:27am UTC](https://isgw-forum.colorado.edu/t/violating-assumptions-of-equal-means-and-variances/343 "2022-06-23T00:27:54Z")
Does anyone know how to handle data where the assumptions for equal means and variances across twin order and zygosity are violated (and any iteration of the possibilities for these assumptions to be violated)? --- ## [Installation of PRSice in Linux](https://isgw-forum.colorado.edu/t/installation-of-prsice-in-linux/371)
**Author:** [@Baraka\_Mkumbe](https://isgw-forum.colorado.edu/u/Baraka_Mkumbe)\ **Replies:** 4\ **Last updated:** [June 21, 2022, 12:04pm UTC](https://isgw-forum.colorado.edu/t/installation-of-prsice-in-linux/371 "2022-06-21T12:04:11Z")
I’m using WSL in window, I want to install PRSice and I have tried to follow the guidelines PRSise’s website with no success. What is the steps by steps procedure to install PRSice in wsl system. Thank you in advance … --- ## [OpenMx Question](https://isgw-forum.colorado.edu/t/openmx-question/370)
**Author:** [@hobbs145](https://isgw-forum.colorado.edu/u/hobbs145)\ **Replies:** 1\ **Last updated:** [June 20, 2022, 8:53pm UTC](https://isgw-forum.colorado.edu/t/openmx-question/370 "2022-06-20T20:53:02Z")
Hello! During the workshop, I only used the R available through the workshop. However, now in my R environment, OpenMx is unable to be loaded (but it is installed). I get the following error: library(OpenMx) Error: pac… --- ## [Ordinal Data—standardized thresholds](https://isgw-forum.colorado.edu/t/ordinal-data-standardized-thresholds/322)
**Author:** [@JuanJMV](https://isgw-forum.colorado.edu/u/JuanJMV)\ **Replies:** 4\ **Last updated:** [June 20, 2022, 3:34pm UTC](https://isgw-forum.colorado.edu/t/ordinal-data-standardized-thresholds/322 "2022-06-20T15:34:08Z")
Hello all, I have a question about ordinal data analysis. I would like to fit a univariate model (1 ordinal variable with 3 categories) in two cohorts (cohort 1 and cohort 2) allowing for sex differences. If I am not wr… --- ## [COPING Day6 DATA](https://isgw-forum.colorado.edu/t/coping-day6-data/349)
**Author:** [@Baraka\_Mkumbe](https://isgw-forum.colorado.edu/u/Baraka_Mkumbe)\ **Replies:** 2\ **Last updated:** [June 20, 2022, 1:27pm UTC](https://isgw-forum.colorado.edu/t/coping-day6-data/349 "2022-06-20T13:27:08Z")
Please can anyone assist on how to copy data for day6(Path to the data) --- ## [Some quick questions, just wondering if I can have a chance to ask these questions after the workshop](https://isgw-forum.colorado.edu/t/some-quick-questions-just-wondering-if-i-can-have-a-chance-to-ask-these-questions-after-the-workshop/366)
**Author:** [@huynguyenacademia](https://isgw-forum.colorado.edu/u/huynguyenacademia)\ **Replies:** 2\ **Last updated:** [June 20, 2022, 11:46am UTC](https://isgw-forum.colorado.edu/t/some-quick-questions-just-wondering-if-i-can-have-a-chance-to-ask-these-questions-after-the-workshop/366 "2022-06-20T11:46:34Z")
Dear Lecturers and Tutors, Thank you for your excellent lectures and tutorings. I still have three quick questions. Though workshops ended, I just wonder if I can ask these questions: In slide 13 (Day 8, pdf on Estim… --- ## [Practical materials for day7&8](https://isgw-forum.colorado.edu/t/practical-materials-for-day7-8/367)
**Author:** [@anonymous11](https://isgw-forum.colorado.edu/u/anonymous11)\ **Replies:** 1\ **Last updated:** [June 18, 2022, 1:47am UTC](https://isgw-forum.colorado.edu/t/practical-materials-for-day7-8/367 "2022-06-18T01:47:01Z")
Hello, Many thanks for all the super helpful lectures and materials! It is a shame that I missed some days of the practical sessions. I wonder is it still possible to get the codes and materials for day7&8 (since the fi… --- ## [Day2 practical answers pdf and video](https://isgw-forum.colorado.edu/t/day2-practical-answers-pdf-and-video/354)
**Author:** [@JessicaTodorov](https://isgw-forum.colorado.edu/u/JessicaTodorov)\ **Replies:** 3\ **Last updated:** [June 17, 2022, 1:57am UTC](https://isgw-forum.colorado.edu/t/day2-practical-answers-pdf-and-video/354 "2022-06-17T01:57:45Z")
Hi Katrina, I am looking for day 2 practical answers and the video walking us through the practical. Could you direct me to where I can find these? Thank you! Jessica --- ## [Small issue in today's code](https://isgw-forum.colorado.edu/t/small-issue-in-todays-code/355)
**Author:** [@ldearaujo](https://isgw-forum.colorado.edu/u/ldearaujo)\ **Replies:** 1\ **Last updated:** [June 17, 2022, 12:42am UTC](https://isgw-forum.colorado.edu/t/small-issue-in-todays-code/355 "2022-06-17T00:42:10Z")
In the file 2022day7.txt, the line: res$pval\<-(1-pt(q=tStat, df = 1887, lower.tail = T))\*2 should actually read: res$pval\<-(1-pt(q=res$tStat, df = 1887, lower.tail = T))\*2 It wouldn’t run without the res$ in the ve… --- ## [Error message run in SSH for day 7 stretch goal 1 GCTA practice](https://isgw-forum.colorado.edu/t/error-message-run-in-ssh-for-day-7-stretch-goal-1-gcta-practice/356)
**Author:** [@anonymous3](https://isgw-forum.colorado.edu/u/anonymous3)\ **Replies:** 2\ **Last updated:** [June 16, 2022, 11:17pm UTC](https://isgw-forum.colorado.edu/t/error-message-run-in-ssh-for-day-7-stretch-goal-1-gcta-practice/356 "2022-06-16T23:17:33Z")
Running below coding in SSH for day 7 stretch goal 1 GCTA practice, I got an error message. gcta64 --pheno ozht.phen --qcovar ozht.prs1.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS1.ACE --reml --reml-est-f… --- ## [Degree of freedom for t-test and interpreting heritability estimate when including PRS as fixed effect](https://isgw-forum.colorado.edu/t/degree-of-freedom-for-t-test-and-interpreting-heritability-estimate-when-including-prs-as-fixed-effect/360)
**Author:** [@anonymous10](https://isgw-forum.colorado.edu/u/anonymous10)\ **Replies:** 3\ **Last updated:** [June 16, 2022, 11:08pm UTC](https://isgw-forum.colorado.edu/t/degree-of-freedom-for-t-test-and-interpreting-heritability-estimate-when-including-prs-as-fixed-effect/360 "2022-06-16T23:08:46Z")
To test the significance of the betas, the df for the t-test is set at 1887. How is this df calculated? When we included PRS as a fixed effect, is the heritability estimate (V(G)/VP) biased as part of the phenotypic var… --- ## [About the 2.5% IBD cutoff?](https://isgw-forum.colorado.edu/t/about-the-2-5-ibd-cutoff/359)
**Author:** [@x.mo](https://isgw-forum.colorado.edu/u/x.mo)\ **Replies:** 1\ **Last updated:** [June 16, 2022, 10:48pm UTC](https://isgw-forum.colorado.edu/t/about-the-2-5-ibd-cutoff/359 "2022-06-16T22:48:12Z")
I am just curious about why 2.5% was chosen, not any other value? --- ## [When to copy the codes for today (day 7)?](https://isgw-forum.colorado.edu/t/when-to-copy-the-codes-for-today-day-7/357)
**Author:** [@huynguyenacademia](https://isgw-forum.colorado.edu/u/huynguyenacademia)\ **Replies:** 0\ **Last updated:** [June 15, 2022, 9:33pm UTC](https://isgw-forum.colorado.edu/t/when-to-copy-the-codes-for-today-day-7/357 "2022-06-15T21:33:24Z")
Hi All, I couldn’t find any codes for today? Can you paste here the path codes to copy files for today. --- ## [What is I . sG2 / m?](https://isgw-forum.colorado.edu/t/what-is-i-sg2-m/353)
**Author:** [@x.mo](https://isgw-forum.colorado.edu/u/x.mo)\ **Replies:** 1\ **Last updated:** [June 15, 2022, 3:39pm UTC](https://isgw-forum.colorado.edu/t/what-is-i-sg2-m/353 "2022-06-15T15:39:09Z")
In the record of “From correlation coefficients to variance components”, slide 15. it was mentioned that in the model, Y = X b + e ; b follows a normal distribution of N(0, I . sG2 / m ). I want to know what is I, S … --- ## [General Information for the tutorial](https://isgw-forum.colorado.edu/t/general-information-for-the-tutorial/348)
**Author:** [@Brad](https://isgw-forum.colorado.edu/u/Brad)\ **Replies:** 0\ **Last updated:** [June 14, 2022, 12:47pm UTC](https://isgw-forum.colorado.edu/t/general-information-for-the-tutorial/348 "2022-06-14T12:47:05Z")
After opening the SSH client (Shell In A Box), make a new folder in your home directory and copy today’s files into that folder: mkdir day6 cp /faculty/brad/2022/day6/\* . Then open Rstudio (RStudio Sign In), and the f… --- ## [Rmz\>2\*rdz](https://isgw-forum.colorado.edu/t/rmz-2-rdz/346)
**Author:** [@jay-sf](https://isgw-forum.colorado.edu/u/jay-sf)\ **Replies:** 1\ **Last updated:** [June 14, 2022, 12:41pm UTC](https://isgw-forum.colorado.edu/t/rmz-2-rdz/346 "2022-06-14T12:41:02Z")
Dear Conor, Dear Dirk We know that "rmz \> 2rdz suggests an ADE model and rmz \< 2rdz suggests an ACE model". How sensitive is this measure, is there a point in choosing and ADE based on e.g. .502 \> 2\*.250? Or in case of… --- ## [Thank you + answers available](https://isgw-forum.colorado.edu/t/thank-you-answers-available/345)
**Author:** [@dirkpelt](https://isgw-forum.colorado.edu/u/dirkpelt)\ **Replies:** 0\ **Last updated:** [June 14, 2022, 11:49am UTC](https://isgw-forum.colorado.edu/t/thank-you-answers-available/345 "2022-06-14T11:49:20Z")
Dear students, thank you all for the great session yesterday! It was great seeing you all working so diligently and staying for the full session, there were great questions and excellent discussions. Note that the work… [Next page](https://isgw-forum.colorado.edu/c/isg-workshops-2022/11.md?page=1)