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 and Flags

    Figure 3-3: Check the boxes for Identifier and Flags to show these fields

  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.

    Launch Hide Show Dialog

    Figure 3-4: Click on the Hide/Show Icon in the tool bar to launch the Column Visibility dialog.

  4. The column visibility dialog should look like Figure 3-5 with the RefSeq Genes 105v2, NCBI column group expanded. See Figure 3-5.

    Set Column Visibility

    Figure: 3-5: Expand and collapse column groups to view the fields in each group. Check or uncheck the boxes to change the visibility of each column or column group.

  5. 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 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 3-6.

    Show HGVS p. notation

    Figure 3-6: Show HGVS p. notation

  6. In addition to modifying source visibility in the table view we can also modify which samples are shown in the table. Initially, the project has all three samples in the table in this order Proband (NA19240), Mother (NA19238), Father (NA19239). If we only want the proband visible in the table then we can quickly make this modification.

    From the Table View tool bar, click on the person icon and select Current. See Figure 3-7.

    Show Only Current

    Figure 3-7: Show only the current sample and not the parents as well

    Now if you scroll to the right in the table you will no longer see the Mother and Father column groups.

  7. By default sample fields are grouped by sample. However, you can change this to have them grouped by field. From that same person icon in the tool bar, select Field Collate. Now the table looks like Figure 3-8.

    Collated by Field Proband Only

    Figure 3-8: Sample fields collated by field for only the proband sample

  8. This isn’t very interesting because we are only showing the current sample (the proband) so go back to the sample visibility menu and select Current + Parents, now it should look like Figure 3-9.

    Collated by Field All Samples

    Figure 3-9: Sample fields collated by field for all samples

    Switch the sample fields back to being collated by sample before moving on.