Changes between Version 6 and Version 7 of xQTLBioinformaticianScript

Timestamp:

2011-09-13T19:12:15+02:00 (13 years ago)

Author:

jvelde

Comment:

--

xQTLBioinformaticianScript

@@ -100 +100 @@
 Data produced during your custom analysis can be written back directly to the database, please look at some existing scripts to see how this is done. 
 However we recommend using XGAP standard functions like: {{{find.<your_xgap_datatype>}}} or {{{add.<your_xgap_datatype>}}}
+
+
+=== Setting up Plink analysis ===
+
+Try the following to see if it works:
+* Install [http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml Plink].
+* Put `plink` on your path.
+* Upload [http://pngu.mgh.harvard.edu/~purcell/plink/hapmap1.zip example data] in your database. (just '''hapmap1.map''' and '''hapmap1.ped''')
+* Create a new ''Analysis'' with target function 'PLINK'.
+* Add an R script with function 'run_PLINK'. Let the script download the MAP and PED example files.
+* Run Plink system call inside R: `plink --noweb --file hapmap1 --assoc --out results`[[BR]]
+* Upload '''results.assoc''' back in database.