User: coleman_jonathan

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Posts by coleman_jonathan

<prev • 38 results • page 1 of 4 • next >
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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 14 months ago by coleman_jonathan370
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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 14 months ago by coleman_jonathan370
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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 20 months ago by coleman_jonathan370
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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 20 months ago by coleman_jonathan370
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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 21 months ago by coleman_jonathan370 • updated 21 months ago by geek_y8.5k
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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 21 months ago by coleman_jonathan370
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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 21 months ago by coleman_jonathan370
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Comment: C: Ways to convert .impute2 to .mldose
... My code at the time you have accessed it would convert 0 0 0 to 0 (which is wrong! I think I assumed a non-call would default to 0.33 0.33 0.33, but it doesn't). This is easily fixable (get it to set 0 0 0 to NA) - I will implement a patch. Thanks for pointing this out! ...
written 2.4 years ago by coleman_jonathan370
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Comment: C: Phenotype choice for one of a MZ twin pair in a genetic association study
... Thanks  - so you would effectively take one phenotype at random, rather than averaging? ...
written 2.4 years ago by coleman_jonathan370
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Power analysis for covariate-adjusted two sample t-test
... I am trying perform a sensitivity analysis to estimate the minimum effect size for a comparison of 100 cases and 100 controls, given 80% power and an adjusted p-value threshold. However, I know this analysis will contain a binary covariate as well. I can't find a power analysis program that allows ...
power statistics t test written 2.7 years ago by coleman_jonathan370 • updated 2.7 years ago by Devon Ryan79k

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Popular Question 29 days ago, created a question with more than 1,000 views. For SNP-set enrichment in GWAS analysis
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: GWAS on dosage data - interaction
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Popular Question 14 months ago, created a question with more than 1,000 views. For Extracting Sample Sizes From The Nhgri Gwas Catalog
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