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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John Meredith, … Michel Nivard4

Nov 20

userGWAS Error in eigen(V_full) : infinite or missing values in 'x'

Hi Michel, Yes, I am estimating S and V with the full genome data, then running the userGWAS function

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userGWAS Error in eigen(V_full) : infinite or missing values in 'x'

Hi Michel, Yes, I am estimating S and V with the full genome data, then running the userGWAS function

Nov 20

Maryam Kazemi, agro...@gmail.com2

Nov 11

LDSC step error

Hi Maryam, The traits listed in the LDSC step should be the munged files (with the .sumstats.gz file

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LDSC step error

Hi Maryam, The traits listed in the LDSC step should be the munged files (with the .sumstats.gz file

Nov 11

Renata Cupertino, … John Meredith6

Nov 1

multivariate GWAS using GenomicSEM - sumstats function

It looks like this worked! Thank you very much for the quick response. Best, John On Friday, November

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multivariate GWAS using GenomicSEM - sumstats function

It looks like this worked! Thank you very much for the quick response. Best, John On Friday, November

Nov 1

Pashupati Mishra, agro...@gmail.com2

Nov 1

Runtime for multivariate GWAS with large number of traits and SNPs

Hi Pashupati, There are two main things you can to do when you have that many SNPs: 1. The estimated

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Runtime for multivariate GWAS with large number of traits and SNPs

Hi Pashupati, There are two main things you can to do when you have that many SNPs: 1. The estimated

Nov 1

Thanh Le, agro...@gmail.com2

Nov 1

userGWAS: warning "some estimated ov variances are negative", NA Qsnp

Hi Thanh Le, Thanks for raising this! The new way of calculating factor-specific Qsnp uses as part of

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userGWAS: warning "some estimated ov variances are negative", NA Qsnp

Hi Thanh Le, Thanks for raising this! The new way of calculating factor-specific Qsnp uses as part of

Nov 1

Joëlle Pasman, … Michel Nivard6

Oct 8

Change in usermodel breaks models that previously ran without issues

Great to hear Joelle, I think this isn't a model you build a paper around but rather a model you

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Change in usermodel breaks models that previously ran without issues

Great to hear Joelle, I think this isn't a model you build a paper around but rather a model you

Oct 8

Maryam Nasserinejad, agro...@gmail.com4

Sep 25

Error in Munge Function: Duplicate Row Names and Embedded Nulls in Summary Statistics

Hi Maryam, It looks like this issue arises only when you use the .gz files as input. Once I unzip

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Error in Munge Function: Duplicate Row Names and Embedded Nulls in Summary Statistics

Hi Maryam, It looks like this issue arises only when you use the .gz files as input. Once I unzip

Sep 25

Apurva Chitre, … Elliot Tucker-Drob7

Sep 24

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

Hi Apurva, While I'm not familiar with standard practices in this area of research, I should say

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

Hi Apurva, While I'm not familiar with standard practices in this area of research, I should say

Sep 24

Pashupati Mishra, Elliot Tucker-Drob2

Sep 23

Summary statistics from GWAS meta-analysis for multivariate GWAS

Please see Calculating Sample Size for Factors here: https://github.com/GenomicSEM/GenomicSEM/wiki/5.

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Summary statistics from GWAS meta-analysis for multivariate GWAS

Please see Calculating Sample Size for Factors here: https://github.com/GenomicSEM/GenomicSEM/wiki/5.

Sep 23

Jujiao Kang, Elliot Tucker-Drob2

Sep 21

Inquiry about calculation of effect in sumstats function

To read the paper introducing Genomic SEM, follow these links: Paper Supplement(Text/Figures)

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Inquiry about calculation of effect in sumstats function

To read the paper introducing Genomic SEM, follow these links: Paper Supplement(Text/Figures)

Sep 21

Lora Pless, agro...@gmail.com2

Sep 20

Thanks for asking this question. The HM3 file is just used for aligning to the same reference allele

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Thanks for asking this question. The HM3 file is just used for aligning to the same reference allele

Sep 20

Sep 10

Error in nrow(SNPs2) : object 'SNPs2' not found

Hello All, I am encountering an issue using userGWAS function for GWAS-by-subtraction with SNP. The

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Error in nrow(SNPs2) : object 'SNPs2' not found

Hello All, I am encountering an issue using userGWAS function for GWAS-by-subtraction with SNP. The

Sep 10

mike, Matthew Yao3

Sep 7

object 'SNPs2' not found

Hello Mike, I want to ask how did you fix this error? I have encountered the exact same error while

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object 'SNPs2' not found

Hello Mike, I want to ask how did you fix this error? I have encountered the exact same error while

Sep 7

Yujia Ma, Elliot Tucker-Drob5

Aug 30

Order of Input in Genomic SEM Analysis

Dear Developer, Thank you so much for your reply. I tried fitting my model without snps. Here's

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Order of Input in Genomic SEM Analysis

Dear Developer, Thank you so much for your reply. I tried fitting my model without snps. Here's

Aug 30

Aug 29

Calculate effective sample size of both latent factors in GWAS by subtraction

Hi there, I am applying GWAS by subtraction as in https://rpubs.com/MichelNivard/565885. In my

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Calculate effective sample size of both latent factors in GWAS by subtraction

Hi there, I am applying GWAS by subtraction as in https://rpubs.com/MichelNivard/565885. In my

Aug 29

Joëlle Pasman, agro...@gmail.com2

Aug 20

Cholesky model runs in 'usermodel' but not 'enrich'

Hi Joelle, Thanks for raising this issue. The problem is that the default behavior for the enrich

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Cholesky model runs in 'usermodel' but not 'enrich'

Hi Joelle, Thanks for raising this issue. The problem is that the default behavior for the enrich

Aug 20

Aug 16

Traits combination for Common Factor/Multivariate GWAS

Dear all, I have general questions regarding the combination of traits for use in common factor/

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Traits combination for Common Factor/Multivariate GWAS

Dear all, I have general questions regarding the combination of traits for use in common factor/

Aug 16

Matthew Yao, … agro...@gmail.com4

Aug 13

GWAS by Subtraction Error

Hi! Sorry for the late response. Thanks for your insights and I have fixed my errors based on your

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GWAS by Subtraction Error

Hi! Sorry for the late response. Thanks for your insights and I have fixed my errors based on your

Aug 13

Nico Ciochetti, Michel Nivard3

Aug 13

Slow userGWAS function

Apologies for the delay in answering, I was testing out different things while troubleshooting

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Slow userGWAS function

Apologies for the delay in answering, I was testing out different things while troubleshooting

Aug 13

Thanh Le, Elliot Tucker-Drob2

Aug 6

Effective sample size for continuous trait

if you list the N as NA and include a column with SNP-specific N, you should be good to go. here is a

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Effective sample size for continuous trait

if you list the N as NA and include a column with SNP-specific N, you should be good to go. here is a

Aug 6

Tomas Gomes, Tania Islam3

Jul 27

commonfactorGWAS parallel processing problem

Hi GenomicSEM teams/users, I'm using GenomicSEM, but it gets stuck for a long time when the

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commonfactorGWAS parallel processing problem

Hi GenomicSEM teams/users, I'm using GenomicSEM, but it gets stuck for a long time when the

Jul 27

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

unread,

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

unread,

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

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