User: Stephanie M. Gogarten

Reputation:
560
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Trusted
Location:
University of Washington
Last seen:
3 days, 8 hours ago
Joined:
6 years, 7 months ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 89 results • page 1 of 9 • next >
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Comment: C: GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for thi
... In the next release of GENESIS, assocTestMM will be deprecated in favor of a new function called assocTestSingle that does not have such strict requirements about chromosome and sex coding. (If you have chromosomes called X and Y and supply a sex column it will do the right thing with frequency, if ...
written 3 days ago by Stephanie M. Gogarten560
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Answer: A: Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems w
... Note that you are using two different paths in the example that worked (with read.vcf) and the example that did not work, so please try using the original file path. vcf.fn <- "/Users/Desktop/batch_1.vcf" seqarray_test1 <- seqVCF2GDS(vcf.fn, "mangrove.gds") ...
written 5 weeks ago by Stephanie M. Gogarten560
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Answer: A: selecting SNPs and samples in GENESIS
... The devel version of GENESIS includes a vignette that may be helpful: http://bioconductor.org/packages/devel/bioc/vignettes/GENESIS/inst/doc/assoc_test_seq.html 1) How many SNPs should be used for KING relationship matrix? We recommend LD pruning to select SNPs. The SNPRelate function snpgdsLDprun ...
written 6 weeks ago by Stephanie M. Gogarten560
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selecting SNPs and samples in GENESIS
... This question was sent by email: We performing GWAS on whole genome data and using GENSIS package for the association analysis. Just a few small Questions: How many SNPs should be used for KING relationship matrix? What is the best way to select number of PCs to be used as covariates? How many SNPs ...
genesis written 6 weeks ago by Stephanie M. Gogarten560
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Comment: C: Replacement for lapply on a GRanges?
... Thanks! I remembered that this thread existed, but failed to find it because I was searching for "lapply" instead of "apply" or "sapply". And I thought it might be useful to have this question answered on the support site. ...
written 3 months ago by Stephanie M. Gogarten560
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Replacement for lapply on a GRanges?
... lapply used to work with GRanges objects in Bioconductor 3.6, but it no longer works in 3.7. What is the recommended replacement? > x <- GRanges(seqnames=c(1,1), ranges=IRanges(start=c(1,10), width=10)) > lapply(x, print) Error in (function (classes, fdef, mtable) : unable to find an in ...
genomicranges written 3 months ago by Stephanie M. Gogarten560 • updated 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... You comment that the problem might be due to the small sample size may be correct. Can you try running the code with a larger dataset? ...
written 4 months ago by Stephanie M. Gogarten560
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... It took a while to chase down where this error is coming from. It turns out to be in the graph package: > showMethods("acc", classes="graph", includeDefs=TRUE) Function: acc (package graph) object="graph", index="character" function (object, index) { nN <- numNodes(object) nNames < ...
written 4 months ago by Stephanie M. Gogarten560
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Answer: A: GENESIS: king2mat: subscript out of bounds
... I think something is wrong with the format of your input files from KING. You can compare them with the example files in the expected format provided with the GENESIS package: "MXL_ASW.kin0" and "MXL_ASW.kin" in the "extdata" directory. Alternatively, you can use the SNPRelate package to run KING in ...
written 4 months ago by Stephanie M. Gogarten560
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GENESIS: king2mat: subscript out of bounds
... Asked by a user via email: I'm interested in using GENESIS package to infer kinship for an ad-mixed population. When I follow steps on as on http://bioconductor.org/packages/release/bioc/vignettes/GENESIS/inst/doc/pcair.R I get error for subscript out of bounds converting king output to matrix. Co ...
genesis written 4 months ago by Stephanie M. Gogarten560

Latest awards to Stephanie M. Gogarten

Popular Question 15 months ago, created a question with more than 1,000 views. For GWASTools
Popular Question 18 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 2.8 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.9 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.0 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 3.0 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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