User: mconomos

gravatar for mconomos
mconomos50
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50
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New User
Location:
University of Washington, Seattle, WA, USA
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1 month, 2 weeks ago
Joined:
4 years, 6 months ago
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m*******@uw.edu

Posts by mconomos

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Error in fitNullMM from GENESIS package on highly-related samples
... Hello. 1) Regarding the very high levels of relatedness: what estimator are you using for your initial kinship coefficient estimates to run PC-AiR? It's either the case that all of your samples are truly very related to each other (so much so that only 3 mutually unrelated samples can be identifie ...
written 6 weeks ago by mconomos50
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Comment: C: Interpreting the output of score test using GENESIS
... 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 9 weeks ago by mconomos50
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Answer: A: GENESIS: ascertainment in GWAS
... 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 4 months ago by mconomos50
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Comment: C: Genesis: doubts with admixMAPMM
... 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 7 months ago by mconomos50
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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 months ago by mconomos50
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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 12 months ago by mconomos50
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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 14 months ago by mconomos50
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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 14 months ago by mconomos50
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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 16 months ago by mconomos50
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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 16 months ago by mconomos50

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Scholar 4.5 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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