User: Stephanie M. Gogarten
Stephanie M. Gogarten • 560
- Reputation:
- 560
- Status:
- Trusted
- Location:
- University of Washington
- Last seen:
- 4 days, 6 hours ago
- Joined:
- 6 years, 3 months ago
- Email:
- s*******@uw.edu
Staff scientist in the Department of Biostatistics
Posts by Stephanie M. Gogarten
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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 15 days 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 15 days 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 17 days 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 17 days ago by
Stephanie M. Gogarten • 560
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Answer:
A: GWASTools vcfWrite function
... Note the warning messages in your output:
1: In getSnpVariable(genoData, id.col) : snp annotation not found
2: In getScanVariable(genoData, sample.col) : scan annotation not found
You need to include scan annotation and SNP annotation in your GenotypeData object in order to get scanID and alleles in ...
written 19 days ago by
Stephanie M. Gogarten • 560
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... Asked by a user via email:
When I used GWASTools to convert gds file to vcf file, my VCF file did not include scanID, allele and allele. Could you let me know why? I used vcfWrite function.
My gds file is imputed gwas 1000 dosage file which created by GWASTools.
Please see the following code and war ...
written 19 days ago by
Stephanie M. Gogarten • 560
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... I think Charlie was expecting gdsSubset to return a new GDS object that he/she can then save, but that is not how the function works. The second argument is the file name of the subsetted GDS file, which is already created by the function. In the example provided, PR5geno_subset contains a character ...
written 19 days ago by
Stephanie M. Gogarten • 560
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Answer:
A: Error converting vcf to gds
... Your version of R is nearly 4 years out of date. Please upgrade to current R and Bioconductor package versions and try again.
...
written 8 weeks ago by
Stephanie M. Gogarten • 560
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... 1. I am not sure if being a string variable is the issue for this error.
Yes, it is. You will need to remove the quotation marks around the intensity/BAF values.
2. What do I denote missing values in normalized x, normalized y, baf and logrrratio values, so intensity and baf files can be uploaded.
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written 8 weeks ago by
Stephanie M. Gogarten • 560
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438
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... Please read the documentation for createDataFile. The description of the "variables" argument is
variables: A character vector containing the names of the variables to
create (must be one or more of ‘c("genotype", "quality", "X",
"Y", "rawX", "rawY", "R", "Theta", "BAlleleFreq" ...
written 3 months ago by
Stephanie M. Gogarten • 560
Latest awards to Stephanie M. Gogarten
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