User: Stephanie M. Gogarten

gravatar for Stephanie M. Gogarten
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University of Washington
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Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 96 results • page 1 of 10 • next >
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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 11 days ago by Stephanie M. Gogarten • 560
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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 22 days ago by Stephanie M. Gogarten • 560
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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 27 days ago by Stephanie M. Gogarten • 560
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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 weeks ago by Stephanie M. Gogarten • 560
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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 weeks ago by Stephanie M. Gogarten • 560
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Answer: A: Using previously calculated PCs in GENESIS
... You can use the SNPRelate package to project relatives onto existing PCs. You would first need to represent your PCs as a snpgdsPCA object, which is a list with elements sample.id, snp.id, eigenval, and eigenvect. See the man pages for snpgdsPCA, snpgdsPCASNPLoading and snpgdsPCASampLoading for more ...
written 7 weeks ago by Stephanie M. Gogarten • 560
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Using previously calculated PCs in GENESIS
... This question was sent by email: I am using the GENESIS package, and I have a question regarding the usage of pcair function. Is there a way to load previously calculated PC values onto pcair function and then use these values to predict PC values for a new set of samples. I know that pcair normal ...
snprelate genesis written 7 weeks ago by Stephanie M. Gogarten • 560
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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 7 weeks ago by Stephanie M. Gogarten • 560
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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 3 months ago by Stephanie M. Gogarten • 560
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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 3 months ago by Stephanie M. Gogarten • 560

Latest awards to Stephanie M. Gogarten

Popular Question 17 months ago, created a question with more than 1,000 views. For GWASTools
Popular Question 20 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 3.0 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: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 3.1 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools
Scholar 3.1 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
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