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 4 months ago by coleman_jonathan420
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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 4 months ago by coleman_jonathan420
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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 4 months ago by coleman_jonathan420 • updated 4 months ago by finswimmer11k
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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 2.3 years ago by coleman_jonathan420
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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 2.3 years ago by coleman_jonathan420
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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 2.8 years ago by coleman_jonathan420
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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 2.8 years ago by coleman_jonathan420
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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 2.8 years ago by coleman_jonathan420 • updated 2.8 years ago by geek_y9.7k
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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 2.8 years ago by coleman_jonathan420
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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 2.8 years ago by coleman_jonathan420

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Appreciated 8 months ago, created a post with more than 5 votes. For A: Ways to convert .impute2 to .mldose
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: GWAS on dosage data - interaction
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Extracting Sample Sizes From The Nhgri Gwas Catalog
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