## User: mconomos

mconomos40
Reputation:
40
Status:
New User
Location:
University of Washington, Seattle, WA, USA
Last seen:
6 days, 4 hours ago
Joined:
4 years, 4 months ago
Email:
m*******@uw.edu

#### Posts by mconomos

<prev • 9 results • page 1 of 1 • next >
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... 1) The score test does not return a beta estimate, but you can get a good approximation of beta by taking Score/(Score.SE^2); or, in your case, by taking Score/Var 2) Score.Stat is the test statistic, which is what you are thinking of when you say "z score variable". The current version of GE ...
written 6 days ago by mconomos40
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... Hello, I understand that your question revolves around accounting for the ascertainment bias from the sampling scheme of families; presumably an affected individual was identified for inclusion in the study and then family members were additionally included, thus leading to the bias. However, I am ...
written 10 weeks ago by mconomos40
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... When analyzing data with 3 or more ancestries (so including 2 or more ancestries in the model), the Joint.Stat and Joint.pval are the test statistic and p-value of the joint Wald test of the null hypothesis that the beta for each ancestry is 0; i.e. that there is no association for any ancestry at t ...
written 5 months ago by mconomos40
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... Hello, Unfortunately GENESIS does not currently have any built in resampling functions, and I'm not aware of any GWAS package that does. Is it possible to use the SKAT code to test one variant at a time by making your aggregation units each variant individually? Sorry I can't be of more help than t ...
written 8 months ago by mconomos40
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... Hello, The results should be very similar. The first question that comes to mind is: are you using the same covariance (relationship) matrix for each software? how did you calculate it? When you say the results are slightly different, could you please elaborate? What is different? and how differe ...
written 10 months ago by mconomos40
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439
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... Sorry, maybe what I was saying wasn't clear (or I'm misunderstanding what you said): It's not that every genotype needs to have a het call, it's that every individual needs to have a het call at some variants being used in your analysis. If that is true, then I'll try to dig some more. A couple fol ...
written 12 months ago by mconomos40
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... Hello, I played around with some sample data, and I have an idea of why you are observing NaN values in your kinMat\$kinship matrix obtained from snpgdsIBDKING(). If I have individuals in my data set who have no observed heterozygous genotype calls at any of the variants being used in the test, then ...
written 12 months ago by mconomos40
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... Hello, How many chromosomes does your species have? Also, are all chromosomes diploid for all individuals? The reason assocTestMM wants sex is so that chromosome 23 (which typically represents the X chromosome in humans) can be coded correctly for males vs. females. If all of your individuals are ...
written 14 months ago by mconomos40
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... Hello, In the code you provided, it looks like you are specifying chr = 19 in the function call to assocTestMM. This will result in only variants in chromosome 19 being tested. Please remove that argument, and chr will default to NULL, which runs all variants. Best, Matt On Mon, Jul 23, 2018 at 1 ...
written 14 months ago by mconomos40

#### Latest awards to mconomos

Scholar 4.4 years ago, created an answer that has been accepted. For A: Why is assocTestMM running with only a fraction of SNPs in genotype data?

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