User: mconomos

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mconomos20
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United States
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2 months, 1 week ago
Joined:
3 years, 10 months ago
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m*******@uw.edu

Posts by mconomos

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain e
... 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 10 weeks ago by mconomos20
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Answer: A: Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
... 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 5 months ago by mconomos20
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... 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 6 months ago by mconomos20
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... 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 6 months ago by mconomos20
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Answer: A: GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for thi
... 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 8 months ago by mconomos20
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Answer: A: Why is assocTestMM running with only a fraction of SNPs in genotype data?
... 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 8 months ago by mconomos20

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Scholar 3.9 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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