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--- userguide:proteinfiltering [2010/03/16 15:10]
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+++ userguide:proteinfiltering [2010/11/05 11:08] (current)
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@@ Line 1: / Line 1: @@
-====== Filter proteins or protein groups ======
+====== How-to filter proteins or protein groups ======
-On a [[userguide:contextdefinition| User Context]] it is possible to apply filters. Filter will mark as //hidden// (or //masked//) protein groups or proteins inside protein groups (depending on user choice) which respect user defined criteria.
+On a [[userguide:contextdefinition| User Context]] it is possible to apply filters. Filter will mark as //hidden// (or //masked//) protein groups or proteins inside protein groups (depending on user choice) according user defined criteria.
-  * If protein groups are filtered, the typical protein is considered but the whole group is (eventually) marked as //hidden//.
+  * If protein groups are filtered (i.e. "Apply to proteins" is NOT checked), the typical protein is considered but the whole group is (eventually) marked as //hidden//.
-  * If proteins are filtered, each proteins of each protein groups are considered and (eventually) marked as //hidden//. If typical protein is set //hidden//, then another sameset protein is set as typical. If there is no more none //hidden// sameset then the whole protein group is set as //hidden//.
+  * If proteins are filtered (i.e. "Apply to proteins" is checked), each protein from every protein groups are considered and (eventually) marked as //hidden//. If a typical protein is //hidden//, then another sameset protein become the typical protein. If there is no more //visible// sameset protein then the whole protein group is set as //hidden//.
-The available filters are described in the how to [[how_to:proteinfiltering|filter proteins [groups] ]].
+The available filters are described in the how-to [[how_to:proteinfiltering|filter proteins [groups] ]].
+If several filters are applied successively, the previous filter(s) is(are) not reset ("cumulative" effect).
 ===== Impact of masking proteins [groups] in algorithms  =====
-Once protein or proteins groups are marked as masked, they will be taken, into account or not depending on operations.
+Once a protein or a protein groups is masked, it will be taken into account is some operations.
-==== Hidden protein groups ====
-In visualization, hidden protein groups will be identified in navigation (context protein groups list).
-The export operations will only work on valid (none hidden) protein groups as well as the Contexts comparison algorithm. The other algorithms
+==== Masked protein groups ====
-(change master / spectral count / protein grouping (peptide to consider) should not be impacted and even if not necessary, they could be applied to all protein groups).
-[ :?: TODO peptides referenced by (only ?) hidden protein groups should be identified in the same way in peptides list]
+In visualization,
+  * masked protein groups will be identified in navigation (see [[userguide:proteingroups|context protein groups]]).
+  * in [[how_to:peptideview|peptides list]], peptides referenced by only hidden protein groups will be identified in the same way.
+The export operations (for AMT or reports) will only export valid (none masked) protein groups. This is also the case for ''Contexts comparison'' algorithm.
-==== Hidden protein ====
+__**The other algorithms (change master / spectral count / protein grouping (peptide to consider) are not impacted and (even if not necessary), they could be applied to all protein groups.**__
+==== Masked proteins====
-Hidden individual protein have more impact as in a //valid// protein group, only some of the proteins may be //valid//.
+If user choose to apply filter on individual proteins, valid protein groups may contains valid and masked proteins.
-In visualization, the protein group view //hidden// proteins are identified.
+In visualization, the [[userguide:proteingroups|protein group view]] identify //masked// proteins in sameset and/or subset lists.
-The export also have to considerate only none hidden proteins when exporting protein groups details or AMT db.
-The contexts comparison algorithm is impacted in the same way as when protein groups are masked : only valid protein should be considered. In the same way, change typical protein does not select //hidden// protein as typical !
-The other algorothms (spectral count / grouping (peptide to consider) should not be impacted).
-===== Hidden proteins group in browser =====
+For the export :
+  * only  valid (none masked) protein are considered when exporting to AMT db.
+  * for reports, only one report is impacted (same subset detail report) and for each protein in valid protein groups, the masked property is indicated.
-===== Hidden proteins in protein groups =====
+  * The ''Contexts comparison'' algorithm is impacted in the same way as when protein groups are masked : only valid proteins should be considered.
+  * ''Change typical protein'' operation does not select //masked// protein as typical !
+__**The other algorithms (spectral count / grouping (peptide to consider) are not impacted.**__

hEIDI

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