User: Stephanie M. Gogarten
Stephanie M. Gogarten • 560
- Reputation:
- 560
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- 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
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... 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. Gogarten • 560
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... 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. Gogarten • 560
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... 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. Gogarten • 560
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... 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 ...
written 6 weeks ago by
Stephanie M. Gogarten • 560
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... 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. Gogarten • 560
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... 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 ...
written 3 months ago by
Stephanie M. Gogarten • 560
• updated 3 months ago by
Hervé Pagès ♦♦ 13k
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... 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. Gogarten • 560
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... 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. Gogarten • 560
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... 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. Gogarten • 560
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... 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 ...
written 4 months ago by
Stephanie M. Gogarten • 560
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