To filter the data that is displayed in a tab pane
By default, when a tab first opens, all data in all available panes is displayed. You can open a Table Filters pane for a selected tab pane which displays all the data (fields) for the pane, and then select from the fields that are listed to filter the pane display to only the data (fields) that meet specific criteria. You can specify the filters for the data that is displayed in a tab pane on a one time only basis, or you can save the filters to a template, and then load the template to filter the data that is displayed in the tab pane anytime as needed. You can also delete a saved filter template.
1. Open the appropriate tab.
2. On the Geneticist Assistant main menu, click Filters > <Tab Pane>. For example, if you clicked Filters with the Sample tab open, then the menu options would be Filters > Sample’s Variants, Filters > Sample’s Status Changes, and so on.
The Table Filters pane opens to the right of the tab. The pane is docked to the right side of the Geneticist Assistant main window. The pane consists of two sub-panes. The left sub-pane displays all the fields for the selected tab pane. The right sub-pane is blank.
3. Repeat Step 2 as many times as needed to open multiple Table Filters panes for the tab.
 | The Table Filters panes are docked from top to bottom in the order in which you opened them. Optionally, to make a Table Filters pane a floating pane, you can click the Undock icon that is in the top right corner of the pane (the icon that is to the left of the Close (x) icon), and then drag the pane. A floating pane is a pane that is visible in the Geneticist Assistant main window, but its location is not confined to a specific area of the window. Instead, you can independently change its size and/or position, including moving the pane outside the main window.To redock the Table Filters pane, click the Close (x) icon to close the pane, and then on the Geneticist Assistant main menu, click Filters and select the tab pane again. |
 | The remainder of this procedure describes how to set up new a data filter. Optionally, below a Table Filters pane, you can click Load Filters to open the Load Filter Template dialog box and select from a list of saved filter templates for the pane. |
4. Click and drag the field by which to filter the data from the list of available fields to the blank pane that is to the right of the list.
An Edit Filter dialog box opens. The name of the selected field is displayed in the Column Name field on the dialog box. The Edit Filter dialog box displays different options depending on the selected filter.
| | The Column Name is a dropdown list that contains all the available fields for the opened tab. You can always select a different field on this list before continuing to Step 5. |
For example:
• If you are filtering data based on a date/time field, then a Relative option is displayed on the Edit Filter dialog box. You select this option to display data from a specified time period that is relative to the current date and time. For example, to display data that has been generated within the last 30 days of the current date and time, select the < operator, select Relative, and then in the Relative field, enter -30 days. (You must enter the minus sign.)
• If you select to filter by Gene, then a Load by phenotype option is displayed on the Edit Filter dialog box. Enter a phenotype to filter by genes that are associated with this phenotype. As you enter the search string, a dropdown list opens. The list is dynamically updated with the phenotypes that are found in the Human Phenotype Ontology database that match the search string.
| | The search string is not case-sensitive, and the string can be found anywhere in the search results. For example, a search string of “thyroid” returns phenotypes of thyroid adenoma and secondary hyperthyroidoism. |
5. On the Operator dropdown list, select the operator for the filter.
Filter Operator | Description |
|---|---|
= | Equals. Must be an exact match to return data. |
≠ | Does not equal. Only data that does not match the value specified is returned. |
> | Greater than. Only data that exceeds the value specified is returned. |
< | Less than. Only data that is less than the value specified is returned. |
>= | Greater than or equal to. Only data that is an exact match for or exceeds the value specified is returned. |
<= | Less than or equals to. Only data that is an exact match for or is less than the value specified is returned. |
contains | Returns data that not only contains the value specified, but also might contain other information. The search string is not case-sensitive. |
does not contain | Returns only the data that does not contain the value specified. The search string is not case-sensitive. |
On | Only data with a date stamp that is the same as the specified date is returned. Identical to the = operator, but used specifically for dates. |
Earlier than | Only data with a date stamp that falls before the specified date is returned. Identical to the < operator, but used specifically for dates. |
Earlier than or on | Only data with a date stamp that is the same as the specified date or that falls before the specified date is returned. Identical to the <= operator, but used specifically for dates. |
Later than | Only data with a date stamp that falls after the specified date is returned. Identical to the > operator, but used specifically for dates. |
Later than or on | Only data with a date stamp that is the same as the specified date or that falls after the specified date is returned. Identical to the >= operator, but used specifically for dates. |
| | The operators that are available on the Operator dropdown list are specific to the type of field that is selected - text, numeric, and so on. Not all operators are available for all field types. |
6. In the Edit Filter dialog box, enter the values for the filter. The dialog box displays different options depending on the selected filter. For example:
• You might have only the option of entering a value in the Value field. If you enter multiple values, then you use a comma to separate multiple values.
• You might have the option of entering a value in the Value field, or clicking a Load Values option to open the Open Text or CSV file dialog box, and then browsing to and selecting the appropriate file.
| | A text file contains a single value. A Comma-Separated Values (CSV) file contains multiple values that are separated by commas. |
7. Click OK.
The Edit Filter dialog box closes. The selected field, its operator, and its value are displayed in the right sub-pane. The filter is applied immediately to the pane.
8. Repeat Step 4 through Step 7 for each field by which the data is to be filtered. When you filter the data by multiple fields, two options are possible:
• You can drag additional fields for filtering on top of an existing filter field to apply the filters on an “and” basis. For example, for the Sample Variant Data sub-tab on the Sample tab, you can add the filter for Coverage >= 300 and then drag the filter for Gene = MSH6 onto the Coverage filter. The results are filtered to show only those variants that have a coverage that is greater than or equal to 300 and that are found in the MSH6 gene.
• You can drag separate additional fields for filtering into the blank pane to apply filters on an “or” basis. For example, for the Sample Variant Data sub-tab on the Sample tab, you can add filters for Coverage >= 300 and a filter for Gene = MSH6. The results are filtered to show those variants that have a coverage that is greater than or equal to 300 or variants that are found in the MSH6 gene.
9. Do any of the following as needed for a specific Table Filter:
• To highlight the results in bright yellow that pass the filtering criteria instead of removing data that fails the filtering criteria, select Highlight.
• The On/Off option is a toggle.
• To remove the applied filters, click On/Off.
• To apply all the filters and view the results onscreen, click On/Off again. (“*Filters Applied” is displayed in the title bar of the affected tab pane.)
| | If the results are not as expected, then this toggling allows you to make the necessary adjustments to a filter before saving it. |
• To remove all the filters that have been applied for the tab pane, click Clear. The filters remain displayed in the Table Filters pane.
| | To clear all filters for all tabs in a single step, on the Geneticist Assistant main menu, click Filters > Clear All Filters. |
• To edit a filter, right-click the filter and on the context menu that opens, click Edit to open the Edit Filter dialog box. Edit the filter (Column, Operator, and/or Value) as needed, and then click OK to close the dialog box and immediately save and apply the edited filter.
• To delete a filter, right-click the filter and on the context menu that opens, click Remove. The pane display is immediately updated.
• To save your filter settings, click Save Filters to open the Save Filter Template dialog box and then do the following:
i Enter a name for the filter template.
ii. If this template is to be available to other users, then select Make template available to other users; otherwise, the template is available only to you.
iii. Click Save.
A Template Save Result message opens, indicating that the new template was saved.
iv. Click OK to close the message and save the filter template to the Geneticist Assistant database.
You, and if applicable, other users, can use this saved filter template to filter the data for this specific tab pane for another project based on the template settings.
10. After you are done filtering the data, you can click Close (x) in the upper right corner of a Table Filter pane to close it.