sciClone annotation file

Question

[benng60]

I am analysing tumour subclones using sciClone (2d mode) and would like to annotate the resulting clusters. What is the R format of the annotation file? Is it a list of lists, or a simple datatable? I cannot get the annotation feature to work. Analysing the [e-mail] output is not very helpful either. Please illustrate using a short example. Thank you very much in advance for your help.

Answer 1

[Chris Miller]

If you're talking about the positionsToHighlight file, it's just a 3-column file. The first two columns should contain chr and pos matching up with the desired points in your input data. If there is a third column with the names to use for labels, then set highlightsHaveNames=TRUE on sc.plot2d.

If that's not what you're talking about, then please provide more information on exactly what you're trying to do, code you're trying to use, etc.