User: Adrienne Stilp

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30
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New User
Location:
United States
Last seen:
1 year, 3 months ago
Joined:
5 years, 6 months ago
Email:
a******@uw.edu

Posts by Adrienne Stilp

<prev • 8 results • page 1 of 1 • next >
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Comment: C: how to save subsetted GDS file
... Hi Charlie, The PR5geno_subset gds file should contain the subset of samples that you requested. Can you provide more infomartion about the problem you're encountering? Are you getting an specific error message? Adrienne ...
written 15 months ago by Adrienne Stilp30
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how to save subsetted GDS file
... Asked by a user via email: Hello, I'm attempting to use the GWAStools package and unfortunately have not had much luck. I have a GDS object and would like to subset that GDS object for specific individuals, and then save the subsetted GDS object permanently in my directory. I'm attempting to use t ...
gwastools written 15 months ago by Adrienne Stilp30 • updated 15 months ago by Stephanie M. Gogarten670
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Comment: C: "set genotype" function for gds?
... The standard missing code for genotype gds files is 3. The GWASTools getGenotype function takes care of converting a value of 3 to NA, but the gdsfmt package does not. When writing the new genotype values, set the missing genotypes to 3 before calling write.gdsn. For example: geno[is.na(geno)] < ...
written 2.5 years ago by Adrienne Stilp30
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Which chromosomes are affected? Are they autosomal, or sex chromosomes? ...
written 2.7 years ago by Adrienne Stilp30
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Comment: C: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
... Can you check if any of the SNPs are monomorphic? In GWASTools, monomorphic SNPs are coded B/B, B/B, etc for all samples (if B is the major allele). I believe PLINK will code monomorphic SNPs as 0/0: from the docs, "If the SNP is monomorphic, by default the allele code out will be 0 and all individu ...
written 2.7 years ago by Adrienne Stilp30
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Answer: A: Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
... You can use the alleleFrequency function in GWASTools for array data or the alleleFrequency function in SeqVarTools for sequencing data. ...
written 3.2 years ago by Adrienne Stilp30
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GWASTools: Sandwich SE
... Hi Arash, The p-values from assocTestRegression are indeed two-sided. (The function uses pchisq to calculate them.) Thanks, Adrienne On Jul 13, 2014, at 10:25 AM, Arash Nazeri wrote: > Dear Adrienne, > > We have been using GWASTools for an interaction model with sandwich standard error ...
gwastools written 5.1 years ago by Adrienne Stilp30
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AnnotatedDataFrame metadata bug?
... Hi Bioconductors, I recently noticed some unexpected behavior for AnnotatedDataFrame metadata. If you have an annotated data frame with metadata and add a new variable whose name is a shortened version of an existing variable, the metadata for the newly-added variable is set to the metadata of the ...
written 5.5 years ago by Adrienne Stilp30 • updated 5.5 years ago by Martin Morgan ♦♦ 23k

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