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6.6 Step 4 - Post processing

6.6.1 Extracting the meta-QTL

Now, suppose we want to get the 7 meta-QTL of the chromosome 1 separetly on the consensus map. To do so, we can use the command QTLModel as follows: 

     $java org.metaqtl.main.QTLModel -m meta-map/consensus_map.xml \
                                     -r meta-qtl/meta-analysis_1_res.txt \
     				-b meta-qtl/meta-analysis_1_best.txt \
     				-o meta-post/metamap.xml
Then, if we use MapView to display the map metamap.xml we obtain something like that:

fig21.png

6.6.2 Projection of the meta-QTL

Finally, it could be useful to project the meta-QTL onto a reference map which provides candidate genes in order to study the congruency between these candidate genes and the meta-QTL.

Then, suppose we want to project the meta-QTL onto the reference map genetic_2005 which we have previously used. So, we can use the program QTLProj as follows: 

     $java org.metaqtl.main.QTLProj -m ref-map/genetic_2005.xml \
                                    -q meta-post/metamap.xml \
     			       -o meta-post/genetic_2005 \
     			       --verbose
Then, if we use MMapView to display the result of the projection we obtain something like that:

fig22.png