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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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Royce Clifford
Feb 14
Finding Neff with only P-value, Odds Ratio, and individual frequencies in a meta-analysis
Hi! I have a meta-analysis with four cohorts, have the total cases and controls for each cohort as
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Finding Neff with only P-value, Odds Ratio, and individual frequencies in a meta-analysis
Hi! I have a meta-analysis with four cohorts, have the total cases and controls for each cohort as
Feb 14
Mingyi Du
,
Michel Nivard
2
Feb 12
Re: Low Neff and mean chi^2 for latent factor in a hierarchical model
Hi Mingyi, Can you provide the model fi/results for the factor model without the SNP for us? What
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Re: Low Neff and mean chi^2 for latent factor in a hierarchical model
Hi Mingyi, Can you provide the model fi/results for the factor model without the SNP for us? What
Feb 12
Patricia Pombo Segura
Feb 10
lavaan warning Model estimation FAILED - userGWAS
Hi all, We are running a multivariate GWAS analysis using the userGWAS() function on a cluster,
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lavaan warning Model estimation FAILED - userGWAS
Hi all, We are running a multivariate GWAS analysis using the userGWAS() function on a cluster,
Feb 10
GenEpiLab
,
Elliot Tucker-Drob
2
Feb 8
SNP effects on the residual (unique) variance
Such a model is not identified but the Qsnp statistic will be very useful here and you can perform
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SNP effects on the residual (unique) variance
Such a model is not identified but the Qsnp statistic will be very useful here and you can perform
Feb 8
Elliot Tucker-Drob
3
Feb 7
Re: [GenomicSEM/GenomicSEM] Question about implied sample size (Issue #100)
you're asking me to make backwards inference about what model you fit and what your parameter
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Re: [GenomicSEM/GenomicSEM] Question about implied sample size (Issue #100)
you're asking me to make backwards inference about what model you fit and what your parameter
Feb 7
Tomas Gomes
,
Elliot Tucker-Drob
2
Feb 6
NEFF Calculations and Relatedness Clarifications
Neff_hat, ie inferred from betas and SEs is the way to go in that sort of situation. We provide
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NEFF Calculations and Relatedness Clarifications
Neff_hat, ie inferred from betas and SEs is the way to go in that sort of situation. We provide
Feb 6
Pashupati Mishra
Jan 13
LD scores and HM3 reference file based on GRCh38
Hi, I was wondering if the EUR LD score data and HM3 reference files also available with GRCh38 build
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LD scores and HM3 reference file based on GRCh38
Hi, I was wondering if the EUR LD score data and HM3 reference files also available with GRCh38 build
Jan 13
Merli Koitmäe
,
agro...@gmail.com
6
12/30/24
QSNP and corresponding pvalues NA
Dear Andrew, They updated GenomicSEM in server, I reran the analysis on some SNPs, but the Q_SNP
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QSNP and corresponding pvalues NA
Dear Andrew, They updated GenomicSEM in server, I reran the analysis on some SNPs, but the Q_SNP
12/30/24
Thanh Le
, …
Elliot Tucker-Drob
3
12/9/24
NaN for estimated SE (both unstandardized and standardized)
It looks like F3 is a higher order factor with two indicators. A two indicator factor is not
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NaN for estimated SE (both unstandardized and standardized)
It looks like F3 is a higher order factor with two indicators. A two indicator factor is not
12/9/24
John Meredith
, …
Michel Nivard
6
12/4/24
userGWAS Error in eigen(V_full) : infinite or missing values in 'x'
Does anyone have any insight on what may be causing these problems or have brainstorming ideas for
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userGWAS Error in eigen(V_full) : infinite or missing values in 'x'
Does anyone have any insight on what may be causing these problems or have brainstorming ideas for
12/4/24
lydia li
,
Elliot Tucker-Drob
5
11/29/24
calculate effective sample size per SNP
In that case you can use the standard liability threshold model and simply enter the relevant
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calculate effective sample size per SNP
In that case you can use the standard liability threshold model and simply enter the relevant
11/29/24
Thanh Le
11/29/24
Model without SNP effects is not identified (df=18) while being identified with SNP effects
Hello everyone, Using 8 traits, I arrived at a hierarchical model with a good fit of CFI being
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Model without SNP effects is not identified (df=18) while being identified with SNP effects
Hello everyone, Using 8 traits, I arrived at a hierarchical model with a good fit of CFI being
11/29/24
Lindsay Melhuish Beaupre
11/26/24
GWAS by subtraction tutorial warning with sumstats command
Hi, I get the following error when I run the sumstats portion of the gwas by subtraction tutorial:
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GWAS by subtraction tutorial warning with sumstats command
Hi, I get the following error when I run the sumstats portion of the gwas by subtraction tutorial:
11/26/24
Matthew Yao
,
agro...@gmail.com
2
11/26/24
Error in nrow(SNPs2) : object 'SNPs2' not found
Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On
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Error in nrow(SNPs2) : object 'SNPs2' not found
Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On
11/26/24
mike
, …
agro...@gmail.com
4
11/26/24
object 'SNPs2' not found
Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On
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object 'SNPs2' not found
Hi Matthew, This should be fixed now if you restart and reinstall the package. Best, Andrew On
11/26/24
Maryam Kazemi
,
agro...@gmail.com
2
11/11/24
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
11/11/24
Renata Cupertino
, …
John Meredith
6
11/1/24
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
11/1/24
Pashupati Mishra
,
agro...@gmail.com
2
11/1/24
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
11/1/24
Thanh Le
,
agro...@gmail.com
2
11/1/24
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
11/1/24
Joëlle Pasman
, …
Michel Nivard
6
10/8/24
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
10/8/24
Maryam Nasserinejad
,
agro...@gmail.com
4
9/25/24
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
9/25/24
Apurva Chitre
, …
Elliot Tucker-Drob
7
9/24/24
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
9/24/24
Pashupati Mishra
,
Elliot Tucker-Drob
2
9/23/24
Summary statistics from GWAS meta-analysis for multivariate GWAS
Please see Calculating Sample Size for Factors here: https://github.com/GenomicSEM/GenomicSEM/wiki/5.
unread,
Summary statistics from GWAS meta-analysis for multivariate GWAS
Please see Calculating Sample Size for Factors here: https://github.com/GenomicSEM/GenomicSEM/wiki/5.
9/23/24
Jujiao Kang
,
Elliot Tucker-Drob
2
9/21/24
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)
9/21/24
Lora Pless
,
agro...@gmail.com
2
9/20/24
Ancestry help
Thanks for asking this question. The HM3 file is just used for aligning to the same reference allele
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Ancestry help
Thanks for asking this question. The HM3 file is just used for aligning to the same reference allele
9/20/24
Yujia Ma
,
Elliot Tucker-Drob
5
8/30/24
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
8/30/24
Andrea Gaudio
8/29/24
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
unread,
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
8/29/24
Joëlle Pasman
,
agro...@gmail.com
2
8/20/24
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
unread,
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
8/20/24
AnnaAP
8/16/24
Traits combination for Common Factor/Multivariate GWAS
Dear all, I have general questions regarding the combination of traits for use in common factor/
unread,
Traits combination for Common Factor/Multivariate GWAS
Dear all, I have general questions regarding the combination of traits for use in common factor/
8/16/24
Matthew Yao
, …
agro...@gmail.com
4
8/13/24
GWAS by Subtraction Error
Hi! Sorry for the late response. Thanks for your insights and I have fixed my errors based on your
unread,
GWAS by Subtraction Error
Hi! Sorry for the late response. Thanks for your insights and I have fixed my errors based on your
8/13/24