====== How to Recompute Retention Time ======

See [[userguide:retentiontimerecomputing|Retention Time Recomputing principles]] if needed.

:!: **If you recompute retention time for a given User context, it will not automatically recompute retention time for child contexts (i.e. contexts under the selected context, if exist).\\
:!: At present, you need to recompute retention time of all your context tree 'manually'. For that, no specific order is needed as final child species are used.**

===== Run the Retention Time Recomputing algorithm =====

{{ :how_to:rtrecomputingmenu.png |}}

:!: **Required conditions to run the Retention Time Recomputing algorithm:**

  * **Selected User context must be grouped**
  * **Protein Grouping on the selected User context must be saved to MSIdb**

If above conditions are respected, then follow these steps:

  - Select the User context for which you want to recompute retention time
  - To display the settings dialog:
      * Right-click on the selected context and select Algorithms→Retention Time→Retention Time Recomputing
      * Or, from the main toolbar, select MS Identifications→Context→Algorithms→Retention Time→Retention Time Recomputing
  - Go to the ''MS Identifications→Context→Algorithms→Retention Time Recomputing'' to display settings dialog
  - Change algo settings options (see below) if needed and click the ''Ok'' button

===== Algo settings options (default options are generally optimal) =====

On top of the dialog, is displayed the User context to process.

**Retention Time Alignment panel**

  * ''Use alignment coefficients'': if you have previously run the [[how_to:alignretentiontime|Retention Time Alignment algorithm]] (on the same UserContext you want to recompute RT) and if you want to take into account the alignment coefficients in the retention time computing, check this option

**Outliers panel**

  * ''Don't take into account outliers'': check this option if you want the algorithm to skip final outliers species (based on [[http://en.wikipedia.org/wiki/Grubbs%27_test_for_outliers|Grubbs method]])

**Computing Method panel**

  * ''Average'': use average to compute the parent species RT from final child species RTs
  * ''Median'': use median to compute the parent species RT from final child species RTs
  * ''Weighted average (by score)'': use average weighted by score to compute the parent species RT from final child species RTs
  * ''Best score per identification + average'': from final child species, take for each identification the RT of the best score species then use average to compute the parent species RT
  * ''Best score per identification + median'': from final child species, take for each identification the RT of the best score species then use median to compute the parent species RT

**Performance panel**

  * ''Use memory tuning'': if NOT selected, the process will be faster but memory consuming. If selected, the process will be a little bit slower but memory efficient.

{{:how_to:rtrecomputinggui.png|}}


===== View the Retention Time Recomputing results =====

Retention times are replaced by new recomputed values for species belonging strictly to the selected User context.\\
:!:**ATTENTION**: if other contexts exist below this selected User context, their species retention times are not recomputed.

{{:how_to:rtrecomputingresult.png|}}