To let the user change the contents of a map layer, you first have to turn on the editing mode for that layer. The layer editing mode is similar to the way transactions are handled in a database:

The changes you make to the layer are held in memory until you decide to either commit the changes to the layer, or roll back the changes to discard them. The following pseudocode is an example of how to implement this using PyQGIS:

layer.startEditing()

# ...make changes...

if modified:
    reply = QMessageBox.question(window, "Confirm",
                                 "Save changes to layer?",
                                 QMessageBox.Yes | QMessageBox.No,
                                 QMessageBox.Yes)
    if reply == QMessageBox.Yes:
        layer.commitChanges()
    else:
        line.rollBack()
else:
     layer.rollBack()

As you can see, we turn on the editing mode for a given map layer by calling layer.startEditing(). As well as set up an internal editing...