User: kylec1729

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kylec17290
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Posts by kylec1729

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Comment: C: Correcting for population substructure in a small sample
... Thanks Kevin. Do you have any references that I can read on how to stratify via bi-plots/regress to `population`? ...
written 1 day ago by kylec17290
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Comment: C: Correcting for population substructure in a small sample
... That's too bad, I guess I kind of figured that. If I decided to do a GWAS or a chromosome-wide AS, is PCA the best method for correcting for this? ...
written 1 day ago by kylec17290
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Correcting for population substructure in a small sample
... I'm running several case-control association analyses on ~50 SNPs with around 1000 cases and 1000 controls. My only "correction" for population stratification so far has been to select only Caucasian British participants, but does this really account for population structure? Are there other things ...
snp written 1 day ago by kylec17290
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Accessing UK Biobank genotype information via patient ID
... How does one access UK biobank genotype information via patient ID? I have extracted SNPs from a gene of interest using PLINK in .bgen+.sample file formats, and now I'd like to be able to view genotype by patient ID (eid), or in some other way, so that I can see if there is any association with the ...
ukbiobank snp written 6 weeks ago by kylec17290
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Comment: C: Finding tag SNPs
... The HWE filtering on HaploView seems a bit odd. For example, there's a SNP that I think would be useful as a tag (which I got from SNPedia and has been implicated with the gene clinically) rs233575 which has a HWpval of around 10^(-14), so very small. The HWpval cutoff is (by default) set to 0.0010, ...
written 6 weeks ago by kylec17290
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Comment: C: Finding tag SNPs
... It is a disease cohort (infectious diseases). I can select SNPs to retain, but I'm not exactly sure what the important things are to look at in selecting these SNPs. For example, 1) do I want a low or high HWpval? 2) Do I want a MAF > 1% (the original is set at 0.1%, which seems a bit low)? The p ...
written 6 weeks ago by kylec17290
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Comment: C: Finding tag SNPs
... Hey Kevin - thanks a lot for the reply. I've been working with your suggestions. I was wondering - how do I decide an appropriate Hardy-Weinberg p value (HWpval) cutoff in HaploView for the purposes described above? There seems to be some desirable SNPs that were left out in the tagging process (the ...
written 6 weeks ago by kylec17290
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Comment: C: Finding tag SNPs
... I'm not sure. I'm looking for just a group of SNPs that just gives a good representation of said gene. eQTL might be useful in terms of seeing what affects the ultimate expression of the protein the gene codes for (and identifying SNPs that are crucial for the expression), but does that necessarily ...
written 6 weeks ago by kylec17290
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Finding tag SNPs
... What is the best way to find tag SNPs associated with particular candidate genes? For example, if I wanted to look at the effects of IFITM3 on influenza patients using their genotype + hospital data, what is the optimal way to find SNPs? I used the UCSC genome browser to find a few randomly chosen S ...
tag snp written 7 weeks ago by kylec17290

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