User: Stephanie M. Gogarten

Reputation:
740
Status:
Trusted
Location:
University of Washington
Last seen:
1 month ago
Joined:
7 years, 10 months ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 122 results • page 1 of 13 • next >
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Answer: A: Why did the Wald test disappear from GENESIS?
... The Wald test done in previous versions of GENESIS was actually an approximation to the Wald test based on the Score test, not an exact Wald test. Because the underlying code of the Score and Wald tests was nearly identical, the only meaningful difference was that the Wald test would return effect s ...
written 4 weeks ago by Stephanie M. Gogarten740
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Why did the Wald test disappear from GENESIS?
... Question received via email: I am currently carrying out association analyses with the GENESIS package. I just wanted to know if there is a reason for the removing of the Wald test option in version 2.16.0. Would you recommend not to use the older versions (and thus the Wald test statistics) of the ...
genesis written 4 weeks ago by Stephanie M. Gogarten740
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Comment: C: Sporadic missingness with admixmmap
... Yes, this is exactly what we do in our own analyses. script 1: ``` nullmod <- fitNullModel(...) save(nullmod, file="my_null_model.RData") ``` script 2: ``` load("my_null_model.RData") adm <- admixMap(admixDataList, nullmod) ``` ...
written 8 weeks ago by Stephanie M. Gogarten740
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Answer: A: Calculating the z score from wald test association results in GENESIS
... See https://support.bioconductor.org/p/125358/#125439 ...
written 9 weeks ago by Stephanie M. Gogarten740
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Comment: C: Interpreting the output of score test using GENESIS
... I'm not entirely sure what you're asking here, since the Score test doesn't give a beta estimate. Is this what you're looking for? https://support.bioconductor.org/p/119621/ ...
written 9 weeks ago by Stephanie M. Gogarten740
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Answer: A: Interpreting the output of score test using GENESIS
... You must be using an old version of GENESIS, but looking at the manual for the current version. `Var` is indeed the variance, and `Score.SE = sqrt(Var)` (no factor of `n`). ...
written 9 weeks ago by Stephanie M. Gogarten740
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Answer: A: Sporadic missingness with admixmmap
... `admixMapMM` cannot handle missing genotype values in the input data. The fastest way to identify which SNPs have missing values is to use the SNPRelate function `snpgdsSNPRateFreq`, which returns missing call rate as well as allele frequency. You could then exclude those SNPs from your analysis. A ...
written 3 months ago by Stephanie M. Gogarten740
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Answer: A: seqVCF2GDS Error Converting VCF to GDS file
... seqVCF2GDS is particular about VCF files conforming to the VCF standard. In this case it looks like the header line for "GMAF" has "Number=A", which means there should be one value per alternate allele. The file itself appears to have a row where there is no alternate allele (hence seqVCF2GDS is exp ...
written 4 months ago by Stephanie M. Gogarten740
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Answer: A: GENESIS: ascertainment in GWAS
... Using a household matrix allows you adjust for the relationship between members of the same family who may not be genetically related (as the latter effect is captured in the kinship matrix), but share common environment, diet, etc. You can create a matrix in which cells for pairs of subjects in the ...
written 4 months ago by Stephanie M. Gogarten740
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Comment: C: sample ids not matching when creating SeqVarData object
... Sorry, I think I was misunderstanding your question. You can use `seqSetFilter` to select a subset of samples for any analysis; you just have to do it *after* creating the `SeqVarData` object. To run regression on a subset of samples, you would do the following: ``` idsToKeep <- phenos$sample.id ...
written 4 months ago by Stephanie M. Gogarten740

Latest awards to Stephanie M. Gogarten

Popular Question 4 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Popular Question 4 months ago, created a question with more than 1,000 views. For Affymetrix CEL files
Scholar 13 months ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Centurion 13 months ago, created 100 posts.
Scholar 13 months ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Popular Question 13 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GWASTools
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 4.1 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 4.1 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 4.2 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 4.2 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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