User: Stephanie M. Gogarten

Reputation:
640
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Trusted
Location:
University of Washington
Last seen:
3 days, 16 hours ago
Joined:
7 years, 3 months ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 110 results • page 1 of 11 • next >
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Comment: C: Genesis: doubts with admixMAPMM
... The "Est" column in the output is the beta estimate. ...
written 20 days ago by Stephanie M. Gogarten640
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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 23 days ago by Stephanie M. Gogarten640
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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 25 days ago by Stephanie M. Gogarten640
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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 The `admixMapMM` function is deprecated, and has been replaced by the `admixMap` function in current versions of GENESIS.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 25 days ago by Stephanie M. Gogarten640
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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 6 weeks ago by Stephanie M. Gogarten640
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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 6 weeks ago by Stephanie M. Gogarten640
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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 6 weeks ago by Stephanie M. Gogarten640
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Answer: A: PCA axis description SNPRelate
... Yes, "principal component (PC)" and "eigenvector" mean the same thing. The element `$eigenvect` has the sample eigenvectors (each row corresponds to a sample). To obtain the SNP loadings, use the function `snpgdsPCASNPLoading`. ...
written 7 weeks ago by Stephanie M. Gogarten640
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Comment: C: GENESIS pcrelate() write gds file doesn't work
... You only need to use `king2mat` to import results from the command-line version of KING (where `file.kin0` and `file.kin` are the paths to text files output by that software). If you are using `snpgdsIBDKING`, you already have the matrix in `king$kinship`. ...
written 8 weeks ago by Stephanie M. Gogarten640
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Comment: C: GENESIS pcrelate() write gds file doesn't work
... `pcrelateToMatrix` takes the entire output object of `pcrelate` (the list of two data.frames) as its first argument: ``` pcmat <- pcrelateToMatrix(mypcrelate) ``` ...
written 8 weeks ago by Stephanie M. Gogarten640

Latest awards to Stephanie M. Gogarten

Popular Question 6 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 23 months ago, created a question with more than 1,000 views. For GWASTools
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 3.5 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.5 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.6 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 3.6 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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