Genomic SEM Users

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Welcome to the Genomic SEM Users google group! You can use this page to post questions about the package, bugs/errors you are experiencing, and feature requests.

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Daniel Rosoff, … Elliot Tucker-Drob6

Jul 16

Sumstats QC filtering

This is detailed in the Grotzinger et al. 2019 publication in Nature Human Behaviour. See "

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Sumstats QC filtering

This is detailed in the Grotzinger et al. 2019 publication in Nature Human Behaviour. See "

Jul 16

Jul 11

Error regarding userGWAS function

Hi all, I ran into problem using userGWAS function. And I'm getting the error regarding infinite

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Error regarding userGWAS function

Hi all, I ran into problem using userGWAS function. And I'm getting the error regarding infinite

Jul 11

Holly Poore, agro...@gmail.com5

Jul 10

NAs for all Q_SNP values

Hi Holly, The model looks right and your correct that the Q_SNP results are specific to each factor.

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NAs for all Q_SNP values

Hi Holly, The model looks right and your correct that the Q_SNP results are specific to each factor.

Jul 10

Jul 7

non-conformable arguments when running userGWAS

Hello evryone! I'm very new to this type of analysis and I've been trying to run the common

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non-conformable arguments when running userGWAS

Hello evryone! I'm very new to this type of analysis and I've been trying to run the common

Jul 7

Giuseppe Fanelli, … giupepp...@gmail.com6

Jun 24

TSEM output: the same gene is reported several times for the same tissue

Many thanks Andrew! best, Giuseppe Il giorno venerdì 10 maggio 2024 alle 19:11:49 UTC+2 agro...@gmail

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TSEM output: the same gene is reported several times for the same tissue

Many thanks Andrew! best, Giuseppe Il giorno venerdì 10 maggio 2024 alle 19:11:49 UTC+2 agro...@gmail

Jun 24

Lucas Perry, agro...@gmail.com3

Jun 14

Can't run any model after update

Hi Lucas, Turns out it was a lavaan update to how it expects certain arguments to be specified. I

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Can't run any model after update

Hi Lucas, Turns out it was a lavaan update to how it expects certain arguments to be specified. I

Jun 14

Yu - Yvonne Huang, Elliot Tucker-Drob2

Jun 3

How to set up the sumstats parameters

I would not typically combine the MTAG-based sumstats with Genomic SEM. MTAG is itself a multivariate

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How to set up the sumstats parameters

I would not typically combine the MTAG-based sumstats with Genomic SEM. MTAG is itself a multivariate

Jun 3

Thanh Le, Michel Nivard2

May 28

How does GenomicSEM merge summary statistics with LD-score files?

Could you share the full log? ITs not uncommon for SNPs to be in one file, but no0t the other, and

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How does GenomicSEM merge summary statistics with LD-score files?

Could you share the full log? ITs not uncommon for SNPs to be in one file, but no0t the other, and

May 28

May 24

GWAS-by-subtraction sumstats genetic correlation

Hi, I run GWAS-by-subtraction and apparently it worked well. However, what I found unexpected is that

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GWAS-by-subtraction sumstats genetic correlation

Hi, I run GWAS-by-subtraction and apparently it worked well. However, what I found unexpected is that

May 24

May 13

Factor loadings in EFA

Dear all, At the moment I am running the exploratory factory analysis (EFA) and follow-up

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Factor loadings in EFA

Dear all, At the moment I am running the exploratory factory analysis (EFA) and follow-up

May 13

Tomas Gomes, agro...@gmail.com3

May 10

Lapack routine dgesv: system is exactly singular

Hi Tomas, Just sent an e-mail response but also wanted to reply here in case others see a similar

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Lapack routine dgesv: system is exactly singular

Hi Tomas, Just sent an e-mail response but also wanted to reply here in case others see a similar

May 10

Anna Deaicy Argoty Pantoja, Elliot Tucker-Drob2

May 9

Common factor plot

You can try this but oftentimes people create them in powerpoint. https://www.alexlishinski.com/post/

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Common factor plot

You can try this but oftentimes people create them in powerpoint. https://www.alexlishinski.com/post/

May 9

Giuseppe Fanelli, Michel Nivard5

May 6

TSEM aggregated Cauchy association omnibus meta-analysis and Miami plot

Many thanks Michel for your useful suggestion! Best, Giuseppe Il giorno venerdì 3 maggio 2024 alle 12

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TSEM aggregated Cauchy association omnibus meta-analysis and Miami plot

Many thanks Michel for your useful suggestion! Best, Giuseppe Il giorno venerdì 3 maggio 2024 alle 12

May 6

AnnaAP, … agro...@gmail.com6

Apr 18

t= 100:00 h CANCELLED AT DUE TO TIME LIMIT ***

Hi Anna, Thanks for responding with the solution! Just to say for others who make look at this thread

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t= 100:00 h CANCELLED AT DUE TO TIME LIMIT ***

Hi Anna, Thanks for responding with the solution! Just to say for others who make look at this thread

Apr 18

yuying li, agro...@gmail.com5

Apr 1

Lapack routine dgesv: system is exactly singular: U[5,5] = 0

Ok so the issue stems from the model prior to including SNPs. Three other things come to mind based

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Lapack routine dgesv: system is exactly singular: U[5,5] = 0

Ok so the issue stems from the model prior to including SNPs. Three other things come to mind based

Apr 1

Apurva Chitre, … Elliot Tucker-Drob5

Mar 27

Genomic SEM v0.0.5 commonfactor() Singular Error with HS Rat Data

V contains squared SEs on the diagonal, so that can easily come from GCTA, but I don't know if

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Genomic SEM v0.0.5 commonfactor() Singular Error with HS Rat Data

V contains squared SEs on the diagonal, so that can easily come from GCTA, but I don't know if

Mar 27

mike, agro...@gmail.com2

Mar 4

Parameter not used (Q_SNP = TRUE)

Did you restart R after reinstalling? I can't reproduce the error on my end with different

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Parameter not used (Q_SNP = TRUE)

Did you restart R after reinstalling? I can't reproduce the error on my end with different

Mar 4

Mar 1

Is it possible to apply SEM to data derived from exonic sources?

The specific article can be viewed at https://www.nature.com/articles/s41586-021-04103-z#Abs1. It

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Is it possible to apply SEM to data derived from exonic sources?

The specific article can be viewed at https://www.nature.com/articles/s41586-021-04103-z#Abs1. It

Mar 1

Holly Poore, Michel Nivard5

Feb 23

discrepancy in results from batch and interactive run

I tried activating the environment in the sbatch script like this: module purge eval "$(conda

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discrepancy in results from batch and interactive run

I tried activating the environment in the sbatch script like this: module purge eval "$(conda

Feb 23

Feb 20

t= 50:00 h CANCELLED AT DUE TO TIME LIMIT ***

Dear all, I have faced difficulties running the step 4 "Combine the summary statistics and LDSC

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t= 50:00 h CANCELLED AT DUE TO TIME LIMIT ***

Dear all, I have faced difficulties running the step 4 "Combine the summary statistics and LDSC

Feb 20

Feb 17

object 'SNPs2' not found

It's really a coincidence. I just sent you an email asking about it, and now it's solved.

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object 'SNPs2' not found

It's really a coincidence. I just sent you an email asking about it, and now it's solved.

Feb 17

Mayra Aldecoa, agro...@gmail.com2

Feb 15

commonfactorGWAS error: " argument 2 matches multiple formal arguments"

I think it's that your second argument is called SNP, but it should be called SNPs (with an s).

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commonfactorGWAS error: " argument 2 matches multiple formal arguments"

I think it's that your second argument is called SNP, but it should be called SNPs (with an s).

Feb 15

Uku Vainik, Michel Nivard4

Feb 14

calculating a subset of genetic correlation matrix

I think you tried the two extremes, namely pairwise and all, I would try to run it in small chunks

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calculating a subset of genetic correlation matrix

I think you tried the two extremes, namely pairwise and all, I would try to run it in small chunks

Feb 14

AnnaAP, … agro...@gmail.com5

Feb 10

Step 3: Prepare the summary statistics for GWAS

Dear Andrew, Thank you for your guidance! The last error was Length of files and linprob should be

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Step 3: Prepare the summary statistics for GWAS

Dear Andrew, Thank you for your guidance! The last error was Length of files and linprob should be

Feb 10

Yu - Yvonne Huang

Feb 8

Negative Genetic correlation in Common Factor GWAS

Dear All, I'm running a CommonFactorGWAS for 4 related traits. The LDSC result shows some traits

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Negative Genetic correlation in Common Factor GWAS

Dear All, I'm running a CommonFactorGWAS for 4 related traits. The LDSC result shows some traits

Feb 8

Shannon Cusack, … Michel Nivard3

Feb 7

Inflated multivariate GWAS pvalues

Hi Shannon, Could you share the model output (without SNPs) so we can try to the set of the potential

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Inflated multivariate GWAS pvalues

Hi Shannon, Could you share the model output (without SNPs) so we can try to the set of the potential

Feb 7

Yu - Yvonne Huang, agro...@gmail.com3

Feb 1

'ReorderModelnoSNP' not found

Dear Andrew, Thank you very much! Now I see what my problem is and the new code runs very well! Best

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'ReorderModelnoSNP' not found

Dear Andrew, Thank you very much! Now I see what my problem is and the new code runs very well! Best

Feb 1

Feng Yu, agro...@gmail.com2

Jan 27

object '"DWLS"' not found

I'm not able to reproduce this error. I'm wondering if the issue is that you have a quote at

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object '"DWLS"' not found

I'm not able to reproduce this error. I'm wondering if the issue is that you have a quote at

Jan 27

Mayra Aldecoa, Jeff Kim3

Jan 24

Get Rs Number Based On Chromosome and Position in GWAS summary statistics

Thanks so much! El lunes, 22 de enero de 2024 a las 14:53:44 UTC-5, kim...@nih.gov escribió: Hi Marya

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Get Rs Number Based On Chromosome and Position in GWAS summary statistics

Thanks so much! El lunes, 22 de enero de 2024 a las 14:53:44 UTC-5, kim...@nih.gov escribió: Hi Marya

Jan 24

Izel Erdogan, Elliot Tucker-Drob2

11/27/23

best model fit based on even chr

Hi Izel, I would recommend that you should follow the standard principles of training and replication

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best model fit based on even chr

Hi Izel, I would recommend that you should follow the standard principles of training and replication

11/27/23

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