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leelabsg / SKAT

Sequence kernel association test (SKAT)
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On half call genotypes and covariates #13

Closed toyanji closed 2 years ago

toyanji commented 3 years ago

Dear Sir, I have two queries on SKAT-O

1.Would it be right to take half call genotypes as missing while generating plink binary files as input for SKAT-O? Since one is doing allelic association, would it be wrong if half call genotypes are treated as haploid?

2.Would it be possible to do skat-O in a case where the covariates such as gender and age are not available?

I hope you will help me with these queries

Regards

Toyanji Joseph

leeshawn commented 2 years ago

Very sorry for the late response.

  1. Since we need genotypes to test, I think it should be treated as a missing
  2. You can run SKAT_Null_Model with 1 as covariate (so the intercept only model). The formula is the same as the formula used in lm function in R. Please refer https://stats.stackexchange.com/questions/211072/how-to-run-lm-function-in-r-but-with-a-formula-with-only-an-intercept
toyanji commented 2 years ago

Dear Sir, Thank you for your reply. I have two queries

1.what is the minimum genotyping rate one can use for skat-o analysis?

2.If one give intercept only model, then how can one specify genotypes as dependent variable just as we use lm function?

Regards

Toyanji Joseph

On Tue, 29 Mar 2022, 08:26 Seunggeun (Shawn) Lee, @.***> wrote:

Closed #13 https://github.com/leelabsg/SKAT/issues/13.

— Reply to this email directly, view it on GitHub https://github.com/leelabsg/SKAT/issues/13#event-6323003073, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF5NFUMARDOQZLSUWBK3ABTVCJWODANCNFSM436IREYQ . You are receiving this because you authored the thread.Message ID: @.***>

toyanji commented 2 years ago

Dear Sir, I am working with binary ped files. How would one generate the SetID, SSD and Info files?I tried to generate SSD file using Generate_SSD_SetID command. I had set the working directory where my binary files are but I got an error message that Error in path.expand(path) :object 'allexome.bed' not found. Please find a screenshot of it in SKAT.jpg along with this mail. When I list the working directory, I have my binary files in the present working directory. Please find the screen shot of it in the ls working directory image. Would you please help me troubleshoot the issue?

regards

Toyanji Joseph

On Tue, Mar 29, 2022 at 10:16 AM Toyanji Joseph @.***> wrote:

Dear Sir, Thank you for your reply. I have two queries

1.what is the minimum genotyping rate one can use for skat-o analysis?

2.If one give intercept only model, then how can one specify genotypes as dependent variable just as we use lm function?

Regards

Toyanji Joseph

On Tue, 29 Mar 2022, 08:26 Seunggeun (Shawn) Lee, < @.***> wrote:

Closed #13 https://github.com/leelabsg/SKAT/issues/13.

— Reply to this email directly, view it on GitHub https://github.com/leelabsg/SKAT/issues/13#event-6323003073, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF5NFUMARDOQZLSUWBK3ABTVCJWODANCNFSM436IREYQ . You are receiving this because you authored the thread.Message ID: @.***>

-- Toyanji Joseph(mob:9899527291) Prof.B.K Thelma's lab Dept of Genetics Biotech centre University of Delhi South Campus Benito Juarez Road New Delhi 110021