project:opensnp

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
project:opensnp [2015/06/06 18:23] – [Doing a PCA w/ openSNP data] gedankenstueckeproject:opensnp [2015/06/06 18:31] (current) – [Team] gedankenstuecke
Line 7: Line 7:
  
 ==== Doing a PCA w/ openSNP data ==== ==== Doing a PCA w/ openSNP data ====
 +[[https://dl.dropboxusercontent.com/u/170329/pca-opensnp.png|{{https://dl.dropboxusercontent.com/u/170329/pca-opensnp.png?350}}]]
 +
 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:
  
Line 66: Line 68:
   * 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, should be fixed   * Right now the scripts for generating all the data are messy at best and can't be run automatically, should be fixed
 +  * Include the 1000Genomes data, not done so far.
   * Go wild!   * Go wild!
 ===== Data ===== ===== Data =====
Line 75: Line 78:
   * [[https://twitter.com/gedankenstuecke|@gedankenstuecke]]   * [[https://twitter.com/gedankenstuecke|@gedankenstuecke]]
   * [[https://twitter.com/ciyer|@ciyer]]   * [[https://twitter.com/ciyer|@ciyer]]
 +  * [[https://twitter.com/podehaye|@podehaye]]
   * and other team members   * and other team members
 ===== Links ===== ===== Links =====
  
   * Repo for doing PCA on openSNP: https://github.com/ciyer/opensnp-fun   * Repo for doing PCA on openSNP: https://github.com/ciyer/opensnp-fun
-   +  * [[https://github.com/gedankenstuecke/opensnp-fun|@gedankenstuecke's fork of ciyer's repo]] 
-{{tag>status:concept needs:dev needs:design needs:data needs:expert}}+  * [[http://www.nature.com/nature/journal/v456/n7218/fig_tab/nature07331_F1.html|The figure we tried to reproduce]] 
 +  * [[https://www.cog-genomics.org/plink2/strat|PLINK manual]] 
 + 
 +{{tag>status:demo needs:dev needs:design needs:data needs:expert}}
  • project/opensnp.1433607788.txt.gz
  • Last modified: 2015/06/06 18:23
  • by gedankenstuecke