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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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Fraction of genes have no gene_p results #518

Open Mathias0077 opened 6 months ago

Mathias0077 commented 6 months ago

Hi Joelle,

I hope you're well. I'd be grateful if you could please help me with a problem in gene based burden testing using the --rgc-gene-p command.

The output to the console reports no issue or problem during the run but in the results file we find the gene_p statistics only for a fraction (~60%) of all genes. I paste you an example output of results (i, gene SPTLC1) with gene_p and (ii, gene SUSD3) without gene_p results. While there is no output of a problem on insufficient data/ rare allele counts or similar, I wonder, what happened and if there might a way to get information about the problem to potentially solve it and to have the gene_p test for all genes? By the way, we cannot observe a pattern, that for example, only for genes with a low number of rare variants the gene_p is not in the results file - this also happens for genes with a higher number of rare variants compared to other genes with a lower number of rare variants and gene_p in the results. And we do the analyses for all autosomal genes for a balanced (1:1) cases/ control outcome.

Any help is highly appreciated.

Thank you, best Mathias

grafik

joellembatchou commented 5 months ago

Hi Mathias,

Can you include the REGENIE log as well as the full sumstats (ie across all masks & tests) for the gene “SUSD3” that has no GENE_P results?

Thank you, Joelle

From: Mathias Gorski @.> Date: Tuesday, April 23, 2024 at 7:32 AM To: rgcgithub/regenie @.> Cc: Subscribed @.***> Subject: [External] [rgcgithub/regenie] Fraction of genes have no gene_p results (Issue #518) Hi Joelle, I hope you're well. I'd be grateful if you could please help me with a problem in gene based burden testing using the --rgc-gene-p command. The output to the console reports no issue or problem during the run but in the results file

Hi Joelle,

I hope you're well. I'd be grateful if you could please help me with a problem in gene based burden testing using the --rgc-gene-p command.

The output to the console reports no issue or problem during the run but in the results file we find the gene_p statistics only for a fraction (~60%) of all genes. I paste you an example output of results (i, gene SPTLC1) with gene_p and (ii, gene SUSD3) without gene_p results. While there is no output of a problem on insufficient data/ rare allele counts or similar, I wonder, what happened and if there might a way to get information about the problem to potentially solve it and to have the gene_p test for all genes? By the way, we cannot observe a pattern, that for example, only for genes with a low number of rare variants the gene_p is not in the results file - this also happens for genes with a higher number of rare variants compared to other genes with a lower number of rare variants and gene_p in the results. And we do the analyses for all autosomal genes for a balanced (1:1) cases/ control outcome.

Any help is highly appreciated.

Thank you, best Mathias

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Mathias0077 commented 5 months ago

Hi Joelle,

thank you for looking into this. The summary stats are those posted in my initial message. I added the logfile to this thread. There are 94 and 35 variants in the genes and the exepected information is provided for both genes:

 -reading in genotypes, computing gene-based tests and building masks...done (xxx ms) 
 -computing association tests...done (xx ms) 
 -computing joint association tests...done (x ms)

the logfiles do not report an error this. I hope this information is helpful.

Best, Mathias

tocheck.log

joellembatchou commented 4 months ago

Hi,

Can you re-run just for gene "SUSD3" including the option --debug? Please send both the output from stdout & stderr.