User: Stephanie M. Gogarten

Reputation:
570
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Trusted
Location:
University of Washington
Last seen:
19 hours ago
Joined:
7 years, 1 month ago
Email:
s*******@uw.edu

Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 101 results • page 1 of 11 • next >
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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 19 hours ago by Stephanie M. Gogarten570
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Comment: C: GENESIS pcrelate() write gds file doesn't work
... Yes, that is correct. ...
written 8 days ago by Stephanie M. Gogarten570
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Comment: C: SeqArray problem in seqVCF2GDS and convert back to vcf
... A few comments/questions: 1. Your R and Bioconductor versions are out of date. We are only able to support the current release (Bioconductor 3.8 for R 3.5). 2. If this problem persists after upgrading, can you share "sample1.vcf" and "sample2.vcf" (or a small subset including the headers and a few ...
written 11 days ago by Stephanie M. Gogarten570
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Answer: A: GENESIS pcrelate() write gds file doesn't work
... The `write.to.gds` argument is no longer an option for pcrelate, because the output format has changed. Previously NxN matrices of kinship and IBD sharing coefficients were returned (or written to GDS) as matrices, but this information is now returned as a pairwise table and can be transformed into ...
written 11 days ago by Stephanie M. Gogarten570
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Answer: A: Imputed dosages in GENESIS
... As of version 2.13.2, GENESIS supports the use of imputed dosages directly from SeqArray GDS files in association testing. Convert a VCF with imputed dosages preserving the dosage field: ``` seqVCF2GDS(vcffile, gdsfile, fmt.import="DS") ``` Then run `assocTestSingle` or `assocTestAggregate` with opt ...
written 5 weeks ago by Stephanie M. Gogarten570
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Answer: A: GENESIS pcrelate() to load gds file and continue where the function broke
... We are actively working on a version of pcrelate that can run in parallel. We hope to have this available in the devel branch of GENESIS by the end of the year. Unfortunately there is no automated way to restart a failed job, but you could try opening the file that was created and seeing which samp ...
written 4 months ago by Stephanie M. Gogarten570
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Comment: C: GENESIS: king2mat: subscript out of bounds
... I'm glad snpgdsIBDKING worked for you. The king2mat function will be deprecated in the next release of GENESIS (in less than 2 weeks), and replaced with a new function kingToMatrix which will hopefully solve your problem with the KING files. ...
written 4 months ago by Stephanie M. Gogarten570
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Comment: C: GENESIS: king2mat: subscript out of bounds
... - specifying "iid=", I obtain error "file("") only supports open = "w+" and open = "w+b": using the former" The order of arguments is king2mat(file.kin0, file.kin=NULL, iids=NULL). So if you tried to provide iids as the second argument without the iids= prefix, it will interpret the argument as a fi ...
written 5 months ago by Stephanie M. Gogarten570
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Answer: A: Imputed dosages in GENESIS
... GENESIS does support imputed dosages, but if you are starting with VCF files there is an extra conversion step involved to get this to work. For imputed dosages in VCF format, use the SeqArray package: use seqVCF2GDS to convert your VCF file to a SeqArray GDS file use seqGDS2SNP with the argument ...
written 5 months ago by Stephanie M. Gogarten570
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Imputed dosages in GENESIS
... Does GENESIS support using imputed dosages instead of discrete genotype calls in association tests? ...
gwastools seqarray genesis written 5 months ago by Stephanie M. Gogarten570

Latest awards to Stephanie M. Gogarten

Popular Question 4 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 21 months ago, created a question with more than 1,000 views. For GWASTools
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 3.3 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.4 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.4 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 3.4 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)

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