User: Stephanie M. Gogarten

Reputation:
660
Status:
Trusted
Location:
University of Washington
Last seen:
2 days, 21 hours ago
Joined:
7 years, 5 months ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 113 results • page 1 of 12 • next >
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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 2 days ago by Stephanie M. Gogarten660
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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 days ago by Stephanie M. Gogarten660
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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 days ago by Stephanie M. Gogarten660
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Comment: C: Genesis: doubts with admixMAPMM
... The "Est" column in the output is the beta estimate. ...
written 12 weeks ago by Stephanie M. Gogarten660
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Comment: C: Genesis: doubts with admixMAPMM
... No, not the way you've set it up here. It is possible to use three separate GDS files instead of a combined one, where each GDS file stores the local ancestry values in the "genotype" node. Then you would create the `GdsGenotypeReader` object with the default value of `genotypeVar="genotype"`. In th ...
written 12 weeks ago by Stephanie M. Gogarten660
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Comment: C: Genesis: doubts with admixMAPMM
... I'm afraid I don't understand your specific question about the data structure above. The example in the manual page is somewhat misleading; if you have three ancestries total, you should only test two of them. I've updated the example here: https://github.com/UW-GAC/GENESIS/blob/master/man/admixMap. ...
written 12 weeks ago by Stephanie M. Gogarten660
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Answer: A: Genesis: doubts with admixMAPMM
... The `admixMapMM` function is deprecated, and has been replaced by the `admixMap` function in current versions of GENESIS. However, I think your questions apply equally to the old and new versions. 1. The `show` method for a GdsGenotypeReader object displays all the information in the GDS file, rega ...
written 12 weeks ago by Stephanie M. Gogarten660
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Answer: A: VCF file does not include snp.id, can I still run SNPRelate for Relatedness Anal
... When the GDS file is created, `snpgdsVCF2GDS` automatically generates a unique integer ID for each variant. This is what you would use to identify variants in SNPRelate functions. ``` snp.id <- read.gdsn(index.gdsn(genofile, "snp.id")) sample.id <- read.gdsn(index.gdsn(genofile, "sample.id")) ...
written 3 months ago by Stephanie M. Gogarten660
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Answer: A: betas for binary outcome
... You have two options for calculating betas for binary outcomes. Option 1) refit the null model including the genotypes for the variant of interest as a covariate. This is a good option if you only need betas for a small number of variants. You can use `SeqVarTools::altDosage` to get the alternate a ...
written 3 months ago by Stephanie M. Gogarten660
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betas for binary outcome
... Question asked via email: I am currently working on a project with a binary outcome, and need to report beta coefficients (representing the log-odds increase per copy of the minor allele), confidence intervals, and odds ratios for each variant. I am using a SeqVarGDSClass object with a SeqVarIterat ...
genesis written 3 months ago by Stephanie M. Gogarten660

Latest awards to Stephanie M. Gogarten

Centurion 8 months ago, created 100 posts.
Scholar 8 months ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 8 months ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Popular Question 8 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 2.1 years ago, created a question with more than 1,000 views. For GWASTools
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 3.7 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.7 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.8 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 3.8 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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