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Getting started with PED

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Input and Edit window revisited

By now you should have an idea how the two windows work

Edit annotations

We switch to Input mode ([Ctrl]+Q), and import the pedigree (press the Import button) we saved on page 3. Now paste the pedigree to the Edit window:

paste onto edit window

In Edit window, press [Ctrl]+N, or select the appropriate menu item

select the annotation window

The annotation window opens. Enter some text. Select a relative font size, and an alignment relative to a cell:

edit annotation

Press OK. Nothing happens ... Now click on the T button in the symbol bar:

Select the 'T' button to select the text annotation

The text you entered is treated as any other (human or line) symbol. You choose the T button to select a text just entered in the annotation window, and you click on a cell that will be the "container" for the text:

text in the edit pane

Delete an annotation in the drawing

Click on the empty symbol button (first column / second row) in the symbol bar. Click on the cell in the drawing where the "container" of the text is located. If you are unsure where this is, show all text containers (reverse these cells):

reverse text cells

The cell containing the text is reversed:

reversed text cell

Now with the "empty" cell in the symbol bar selected, click on the reversed cell in the window:

delete cell

Press [Ctrl]+R to redraw, thus removing the remnants of the previously deleted text.

Options in Edit and Input mode

If you choose (in Input mode) Input window - Options - More ... or (in Edit mode) Screen - View, you get the following dialog:

View options

These options should be rather self explaining. If in doubt, please press the Help button.

Adding a legend

You can add a legend manually: Click at the appropriate symbol in the symbol bar, click on the edit window to draw the symbol, right click on the symbol, and enter the appropriate legend. As an alternative, you can do it automatically:

Add legend automatically

Now you get a , well, simple legend for a simple pedigree:

legend

PED scans all symbols in the pedigree, and shows each symbol that is not white / empty. The legend text is taken from the phenotype menu. Since we previously chose "left filled" from the phenotype menu, this is what the legend will say:

phenotype menu

now you can right click on this symbol to edit the legend text:

edit legend

This is the legend:

the legend

Consider editing input text labels and phenotype menu items

... when data from pedigrees entered by different persons should be collected in a single database.

This does not look like a big deal with this simple pedigree from above. But consider counceling cancer families. You can edit the phenotypes menu items as well as all corresponding symbols just as you like (for details take a look at the how-to resources). Then phenotype #4 is no longer "left filled" but, say, "HNPCC". And phenotype #26 may be not just "bottom left white", but a red symbol labelled "breast cancer", and so on. Even easier to change are the labels of the "Text and haplotypes" dialog:

edit dialog labels

Then in the dialog no longer "Text 1" but a more meaningful "First name" or "day of birth" will be displayed, and instead of "M1", e.g, the name of the marker you used:

edit labels

Now, when you right click on a symbol in the input or in the edit window, more meaningful labels for the input fields will be dsplayed:

new dialog with more meaningul labels

When these edited labels and phenotype menu items are made available to all PED useres involved in the same investigation (even at different locations), they all can export their pedigrees, e.g. as a CSV file, where each family member has an unique ID (preserved even after multiple im-/exports), and all exported files carry the same kind of information in their respective columns.

The file menu: Save the pedigree as an editable layout (PED) file or as Windows metafile (WMF) for import into a presentation or text program

From the file menu select Save as... and enter the name of the pedigree. A file suffix of "PED" will it make editable in the edit window in PED. A file suffix "WMF" will create a Windows Metafile:

file menu

Enter the name of the pedigree. Please do not miss to enter the suffix (ped or wmf) as well:

enter someName.WMF

If you save as a Metafile, you may want to have a colored background:

enter background

Press OK. Now create a new text document (This is an example with OpenOffice.org), and insert a picture from file:

Insert metafile in OpenOffice.org

Finally, here is the metafile (it will work in MS Word, or in presentation programs like MS Powerpoint as well...), ready to be resized, from stamp to poster size.

Metafile imported in OpenOffice.org

No need to mention ...

... PED can print pedigrees at any size on each paper size. It is nice to print a large pedigree in poster size - but most of the time you probably print a pedigree on your own office printer. PED uses always one sheet of paper, no matter what the paper size is.

Thank you for reading Getting started !

Now you should know enough about PED to start drawing. Later on, you may want to take a look at the Import / Export part, the How-To resources, and the FAQs.

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