User: Stephanie M. Gogarten

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530
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University of Washington
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Staff scientist in the Department of Biostatistics

Posts by Stephanie M. Gogarten

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Importing affymetrix genotype calls with GWASTools
... 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 7 days ago by Stephanie M. Gogarten530
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Answer: A: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
... Something must have changed in devel in one of the packages SeqArray depends on. With SeqArray 1.9.4 but release versions of all its dependencies, SeqArray::info() still returns a CharacterList for AA. I will look into it, but I'm about to go on vacation so I won't have an answer for you until Janua ...
written 8 weeks ago by Stephanie M. Gogarten530
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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 3 months 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 6 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 8 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 8 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 12 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 14 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 14 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 14 months ago by Stephanie M. Gogarten530

Latest awards to Stephanie M. Gogarten

Popular Question 11 months ago, created a question with more than 1,000 views. For Error in biocLite("BiocUpgrade") when trying to update to latest release
Scholar 2.2 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.3 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.4 years ago, created an answer that has been accepted. For A: Error in importing signals with createAffyIntensityFile (GWASTools)
Scholar 2.4 years ago, created an answer that has been accepted. For A: Importing affymetrix genotype calls with GWASTools

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