User: coleman_jonathan
coleman_jonathan • 330
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Posts by coleman_jonathan
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... Above link is dead: see [this Biostars answer][1]
[1]: https://www.biostars.org/p/133204/ ...
written 5 months ago by
coleman_jonathan • 330
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... 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 5 months ago by
coleman_jonathan • 330
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... 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 11 months ago by
coleman_jonathan • 330
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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 11 months ago by
coleman_jonathan • 330
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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 11 months ago by
coleman_jonathan • 330
• updated
11 months ago by
geek_y ♦ 7.7k
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... **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 ...
written 11 months ago by
coleman_jonathan • 330
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... 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 12 months ago by
coleman_jonathan • 330
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... 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 20 months ago by
coleman_jonathan • 330
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... Thanks - so you would effectively take one phenotype at random, rather than averaging?
...
written 20 months ago by
coleman_jonathan • 330
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... 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 ...
written 22 months ago by
coleman_jonathan • 330
• updated
22 months ago by
Devon Ryan ♦ 70k
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