User: Stephanie M. Gogarten

Reputation:
720
Status:
Trusted
Location:
University of Washington
Last seen:
4 days, 13 hours ago
Joined:
7 years, 8 months ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 120 results • page 1 of 12 • next >
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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 4 days ago by Stephanie M. Gogarten720
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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 10 days ago by Stephanie M. Gogarten720
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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 12 days ago by Stephanie M. Gogarten720
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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 12 days ago by Stephanie M. Gogarten720
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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 5 weeks ago by Stephanie M. Gogarten720
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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 9 weeks ago by Stephanie M. Gogarten720
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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 12 weeks ago by Stephanie M. Gogarten720
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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 3 months ago by Stephanie M. Gogarten720
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Answer: A: sample ids not matching when creating SeqVarData object
... You can't use the `seqSetFilter` function to change the order of samples read from the GDS file, or to assign `sampleData` to only a subset of samples in the GDS file. The `AnnotatedDataFrame` you use to create a `SeqVarData` object must contain the same samples, in the same order, as the GDS file. ...
written 3 months ago by Stephanie M. Gogarten720
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sample ids not matching when creating SeqVarData object
... Question submitted by email: I’m trying to use the regression function in SeqVarTools but I keep getting error about sample id’s not matching when creating SeqVarData, e.g. ``` # Get the sample ids and force them to match sampleIds <- data.frame( sample.id=seqGetData(gds, 'sample.id') ) phenos ...
seqvartools written 3 months ago by Stephanie M. Gogarten720

Latest awards to Stephanie M. Gogarten

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Affymetrix CEL files
Scholar 11 months ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Centurion 11 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Popular Question 11 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 2.3 years ago, created a question with more than 1,000 views. For GWASTools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 3.9 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.9 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 4.0 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 4.0 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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