User: coleman_jonathan
coleman_jonathan • 420
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Posts by coleman_jonathan
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... That can be assumed (in that it would be straightforward to ensure the file is formatted in that way) ...
written 19 months ago by
coleman_jonathan • 420
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... 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 19 months ago by
coleman_jonathan • 420
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... 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 ...
written 19 months ago by
coleman_jonathan • 420
• updated
19 months ago by
finswimmer ♦ 13k
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... Above link is dead: see [this Biostars answer][1]
[1]: https://www.biostars.org/p/133204/ ...
written 3.6 years ago by
coleman_jonathan • 420
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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 3.6 years ago by
coleman_jonathan • 420
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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 4.0 years ago by
coleman_jonathan • 420
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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 4.1 years ago by
coleman_jonathan • 420
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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 4.1 years ago by
coleman_jonathan • 420
• updated
4.1 years ago by
geek_y ♦ 11k
4
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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 4.1 years ago by
coleman_jonathan • 420
3
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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 4.1 years ago by
coleman_jonathan • 420
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