User: coleman_jonathan

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Posts by coleman_jonathan

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Calculate average parental genotype
... That can be assumed (in that it would be straightforward to ensure the file is formatted in that way) ...
written 12 days ago by coleman_jonathan410
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Comment: C: Calculate average parental genotype
... Thanks - have added. My concern is less the method to do so in R (if we end up doing that, I'll add the code as an answer), but more whether there's a less computationally-intensive / more sophisticated method that I'm missing. ...
written 12 days ago by coleman_jonathan410
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Calculate average parental genotype
... I am interested in creating an averaged value for genotype across two parents: E.g. Input (three unrelated couples, 1, 2 and 3): Individual SNP1 SNP2 SNP3 SNP4 ... Father_1 1 0 1 2 ... Mother_1 0 0 2 1 ... Father_2 ...
gwas snp written 12 days ago by coleman_jonathan410 • updated 12 days ago by finswimmer10k
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Comment: C: What Are Good Values For R^2 And D' For Linkage Disequilibrium
... Above link is dead: see [this Biostars answer][1] [1]: https://www.biostars.org/p/133204/ ...
written 23 months ago by coleman_jonathan410
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Comment: C: Ways to convert .impute2 to .mldose
... This is less straightforward - the information metrics produced by these programs are not totally equivalent, although highly correlated (see Marchini and Howie, 2010 [www.nature.com/nrg/journal/v11/n7/extref/nrg2796-s3.pdf][1]). The files themselves are also structured differently: mlinfo: SN ...
written 23 months ago by coleman_jonathan410
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Answer: A: Using family data in Mixed Linear Model Association Analyses (MLMA)
... For anyone interested in the answer to this question, look at Jian Yang's response here: [http://gcta.freeforums.net/thread/323/family-data-mlma][1] [1]: http://gcta.freeforums.net/thread/323/family-data-mlma ...
written 2.4 years ago by coleman_jonathan410
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Answer: A: GWAS with few samples
... Assuming your QT is a genuine continuous variable, you should use the QT. It has greater power (read this: [http://www.ncbi.nlm.nih.gov/pubmed/11987478][1]) [1]: http://www.ncbi.nlm.nih.gov/pubmed/11987478 ...
written 2.5 years ago by coleman_jonathan410
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Answer: A: awk to clip off telomeres
... This seems like more of a sed query than an awk one. Specific solution to your query below: sed -e 's/^CCCCAAAACCCC//g' inputfile.txt > outputfile.txt (This removes the sequence of `CCCCAAAACCCC` from the beginning of any line). The general solution (which I imagine is what you really wan ...
written 2.5 years ago by coleman_jonathan410 • updated 2.5 years ago by geek_y9.1k
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Using family data in Mixed Linear Model Association Analyses (MLMA)
... **Background:** Using multiple genomic relatedness matrices (GRMs; one for the whole cohort, and one just capturing familial relationships), it is possible to capture SNP-heritability in family data (as detailed on the GCTA forums and in Zaitlen et al, 2013: [http://gcta.freeforums.net/thread/241/gc ...
genome mlma family gcta written 2.5 years ago by coleman_jonathan410
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Answer: A: PRSice polygenic score with only controls
... This a known bug - no regression still requires a non-missing phenotype. I recommend you run PRSice with a dummy phenotype file as you describe and the no regression option on ...
written 2.5 years ago by coleman_jonathan410

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Popular Question 23 months ago, created a question with more than 1,000 views. For Extracting Sample Sizes From The Nhgri Gwas Catalog
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