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Applying a Genetic Marker Map to a Spreadsheet

4.6 Applying a Genetic Marker Map to a Spreadsheet

A genetic marker map can be applied to a spreadsheet with marker names as either column name headers or row labels. To do so select File > Apply Genetic Marker Map from the spreadsheet menu.

In order to apply a genetic marker map you first need to have the desired marker map in the marker maps folder. All markers that can be mapped will be reordered in marker map order by chromosome first and then position. Any markers that cannot be mapped will be moved to the beginning of the spreadsheet and the marker map fields will be left blank.

Selecting a Genetic Marker Map

All available marker maps in the program Marker Maps folder are displayed in the list box (see Figure 24) with several parameters to aid in determining the best marker map to use. If there are several versions of a marker map, the number of markers in the map, the last date modified or the field names available will indicate any differences between the two versions. The columns can also be reordered by left-clicking on the column header and dragging to the left or the right.

Setting Apply Options

Normally, if the spreadsheet has multiple markers with the same name, it will be reordered so that the markers with the same name are adjacent and all markers in the spreadsheet contained in the marker map will contain the map information in the marker map fields.

Checking the “Drop duplicate markers” will, on the other hand, map the first occurrence of any marker contained in the marker map and delete all other occurrences of the same marker from the mapped spreadsheet.

Indicating Direction to Apply Genetic Marker Map

Marker names can either be column headers or row labels. It is important to select the right option for the spreadsheet to be mapped. If the wrong option is selected, an error message indicates that no columns or rows could be mapped. If both column headers or row labels are marker names, the map can be applied to only one option but not both.

In order to plot data and have the genetic annotation tracks visible, the marker names need to be row labels and the marker map needs to be applied as such, see Genome Browser. If the marker map is applied to column headers, the spreadsheet can be transposed and the marker map information will be transposed as well without the need to reapply, see Transposing Spreadsheets.

Applying a Different Genetic Marker Map

A marker map can be changed by applying a new marker map to a previously marker mapped spreadsheet. A new navigator spreadsheet node will be created with the new marker map as a child of the original marker mapped spreadsheet. If the spreadsheet with the old marker map applied is no longer needed in the spreadsheet, a top-level spreadsheet could be created for the new marker mapped spreadsheet. Then all the unnecessary nodes can be deleted. See Create Top-Level Spreadsheet for more information.

Dropping a Genetic Marker Map from a Spreadsheet

Sometimes it might be desirable to remove a marker map from a marker mapped spreadsheet. This can be done by selecting File > Drop Genetic Marker Map from the spreadsheet menu. A child node is created as a descendant of the marker mapped spreadsheet.