User: Stephanie M. Gogarten

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530
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Location:
University of Washington
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2 weeks, 2 days ago
Joined:
5 years, 9 months ago
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Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 72 results • page 1 of 8 • next >
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Answer: A: Question on 'gdsSubset' function
... You can use put.attr.gdsn to define the genotype node as "snp.order" (snp x sample) or "sample.order" (sample x snp). library(gdsfmt) gfile <- createfn.gds("test.gds") gen_node <- add.gdsn(gfile, "genotype", storage="bit2", valdim=c(20, 10)) #20 snps, 10 scans=samples put.attr.gdsn(gen_node, " ...
written 29 days ago by Stephanie M. Gogarten530
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Answer: A: Creating Intensity GDS file for the R package GWAStools
... From a quick look at the documentation for crlmm, I think the "R" and "G" intensities output by readIdatFiles are analogous to the raw X and Y intensities output by Illumina's GenomeStudio (which is what we based the GWASTools input on). You will want to normalize the intensities before using them f ...
written 3 months ago by Stephanie M. Gogarten530
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Comment: C: Error using readVcf
... You make a good point about the file communication, but unfortunately VariantAnnotation only takes VCF files as input, so it's up to every other package author to write a coercion method to a VCF object. Based on my experience with doing this for the SeqArray package, that's a substantial amount of ...
written 5 months ago by Stephanie M. Gogarten530
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Answer: A: Error using readVcf
... Look at getAlleleA(genoData) and getAlleleB(genoData) to see where the non-nucleotide characters are coming from. You might need to correct the "alleleA" and "alleleB" columns in the SNP annotation attached to genoData. ...
written 5 months ago by Stephanie M. Gogarten530
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Answer: A: "set genotype" function for gds?
... You need to use the gdsfmt package to modify GDS files directly. library(gdsfmt) file <- system.file("extdata", "illumina_geno.gds", package="GWASdata") gdsfile <- tempfile() file.copy(file, gdsfile) # open file in write mode gdsobj <- openfn.gds(gdsfile, readonly=FALSE) # get node of ...
written 9 months ago by Stephanie M. Gogarten530
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... I'm not sure what's going on here, but you can try a few things to troubleshoot: 1) check that the "alleleA" and "alleleB" columns in your SNP annotation are correct 2) run "plinkCheck" to compare the file you produced to the original GDS 3) use SNPRelate::snpgdsGDS2BED and see if you have the sa ...
written 11 months ago by Stephanie M. Gogarten530
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... I suspect the difference in P-values is due to the difference in the way plink codes the X chromosome for males: http://pngu.mgh.harvard.edu/~purcell/plink/faq.shtml#faq9 GWASTools codes males as (0,2), while plink codes them as (0,1). Also GWASTools does not adjust the P-values, so in the plink o ...
written 11 months ago by Stephanie M. Gogarten530
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... The "alleleFrequency' function in GWASTools will ignore heterozygotes for males on the X chromosome, but assocRegression does not set any genotypes to missing automatically. I would suggest using the "hetBySnpSex" function to identify X chrom SNPs with high heterozygosity in males and filter those f ...
written 11 months ago by Stephanie M. Gogarten530
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... If you are applying exactly the same filters and methods the results should be the same. It seems likely that either GWASTools or PLINK or both is not doing exactly what you think it's doing (different default options, perhaps). Are you certain that the samples and SNPs in both your GDS and PLINK fi ...
written 11 months ago by Stephanie M. Gogarten530
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Answer: A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... GenomeStudio does calling of genotypes, meaning it takes the idat files and determines the genotype of each of your samples for each SNP on the array. It can output the resulting genotypes, as well as the intensity values that were used to call them, as plain text files. It sounds like you already h ...
written 18 months ago by Stephanie M. Gogarten530

Latest awards to Stephanie M. Gogarten

Popular Question 8 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 2.0 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.0 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.1 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.1 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools

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