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project:opensnp [2015/06/06 18:23] – [Doing a PCA w/ openSNP data] gedankenstuecke | project:opensnp [2015/06/06 18:31] (current) – [Team] gedankenstuecke | ||
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==== Doing a PCA w/ openSNP data ==== | ==== Doing a PCA w/ openSNP data ==== | ||
+ | [[https:// | ||
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This is done in multiple steps with the help of PLINK and SmartPCA: | This is done in multiple steps with the help of PLINK and SmartPCA: | ||
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* The plots here were done on all SNPs, not the subsampled ones (as I didn't notice that it wasn't done automatically…). Should re-run it on the less autocorrelated set | * The plots here were done on all SNPs, not the subsampled ones (as I didn't notice that it wasn't done automatically…). Should re-run it on the less autocorrelated set | ||
* Right now the scripts for generating all the data are messy at best and can't be run automatically, | * Right now the scripts for generating all the data are messy at best and can't be run automatically, | ||
+ | * Include the 1000Genomes data, not done so far. | ||
* Go wild! | * Go wild! | ||
===== Data ===== | ===== Data ===== | ||
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* [[https:// | * [[https:// | ||
* [[https:// | * [[https:// | ||
+ | * [[https:// | ||
* and other team members | * and other team members | ||
===== Links ===== | ===== Links ===== | ||
* Repo for doing PCA on openSNP: https:// | * Repo for doing PCA on openSNP: https:// | ||
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- | {{tag> | + | * [[http:// |
+ | * [[https:// | ||
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+ | {{tag> |