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 sco@vafs.merged output is not very helpful either. Please illustrate using a short example. Thank you very much in advance for your help.
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written
by
benng60 •
1 answer
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.
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written
by
Chris Miller
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