3. The Table View InterfaceΒΆ

Highlighted Filter View

Figure 3-1: The VarSeq window with the filter view highlighted and detailed

  1. The table view (Figure 3-1) in VarSeq can have numerous columns from the various data sources. To make these columns or data fields easier to work with, they are grouped by source. Columns and column groups can be hidden or shown to make the fields or sources more easily accessible.

    First, we will show you two different ways to hide and show columns and column groups.

    Right-click on any column, for example Identifier and select Hide. All column groups with the exception of sample column groups can be hidden in this manner as well. See Figure 3-2.

    Hide Identifier Column

    Figure 3-2: Right-click on the Identifier column and select Hide.

  2. The visibility of fields for a particular column group can be quickly modified by hovering

    over the column group and right clicking to see all the fields available. Check the Identifier box to show it again. See Figure 3-3.

    Show Identifier

    Figure 3-3: Check the box for Identifier to show the field in the table

  3. Another way to hide and show columns and column groups is to use the Hide/Show or Column Visibility dialog. This dialog allows you to quickly select which columns to see or not see as well as to show hidden columns or column groups. Click on the eye icon in the tool bar to launch the dialog. See Figure 3-4. The column visibility dialog should look like Figure 3-4 with the RefSeq Genes 105v2, NCBI column group expanded.

    Launch Hide Show Dialog

    Figure 3-4: Click on the Hide/Show Icon in the tool bar to launch the Column Visibility dialog. Expand and collapse column groups to view the fields in each group. Check or uncheck the boxes to change the visibility of each column group.

  4. Expand the Transcript Interactions RefSeq Genes 105v2, NCBI column group, click on Unselect All to the right of this column group name and then click on the transcript interactions RefSeq Genes 105v2, NCBI box, finally, click on the box in front of HGVS p. and then click OK. This will show the column group but only have the “P.” notation column visible. See Figure 3-5.

    Set Column Visibility

    Figure: 3-5: Show HGVS p. notation

  5. Tables can either updated when filter results are clicked on or they can be fixed to a particular filter result. To tell if a table is locked to a particular filter, examine the table filter icon. If the padlock icon is open the table is unlocked. If it is closed, then it is locked to the particular result identified in the icon. See Figure 3-6.

    unlocked table

    Figure 3-6: The current table shows the results from the current filter chain but it is not locked.

    Click on the final result of the filter chain. The table filter icon should now say “Cardiomyopathy Input”. We want to keep a copy of this table a create another table to explore intermediate results. So, click the lock icon to lock the current table then click the clone icon in the Table View tool bar. This will lock the current table and create a copy. See Figure 3-7.

    Table before cloning
    Cloned Locked table

    Figure 3-7: Clone the current table to lock it to the filter chain results and create another locked table.

    Click the table for the copy to bring it to the front and unlock the filter view then click on the filter results for the Effect (Combined) filter card. You should see the top table update to include all 82 variants from that card, however, the bottom table locked to Cardiomyopathy does not update. See Figure 3-8.

    Updated Unlocked table but not locked

    Figure 3-8: Clicking on intermediate results updates the unlocked table but does not update the locked table

    Click around some more, expand some cards and see how the table updates.

    Click on the Gene Rank filter card and expand it. Now right-click on the Greater than 0.9 category and select Results Up Through This Expression. This will update the table to be all variants for the current sample that match our phenotype of interesting (cardiomyopathy) from the original input set of variants. See Figure 3-9.

    Results up through this Expression

    Figure 3-9: Display all of the variants for the current sample that match the cardiomyopathy phenotype from the original input set of variants

    See in Figure 3-10 how the table filter icon changes to indicate a particular category was used for the variants to display in the table. See Figure 3-10.

    Cardiomyopathy Variants

    Figure 3-10: All variants matching the cardiomyopathy phenotype in the table view