SciClone R package

Question

[e.j.m.noureldeen]

Hi, I am trying to use SciClone package for using VAF and CNV data to define the major clones in matched samples and in different samples in the same cohort as well... I have some questions please as I am new to it .. 1) In the (Sciclone) functions , "CopyNumberCalls" requires a column called (Copy number value for the segment) would you explain to me what is this mean and how to calculate it ?? 2) in the 2d plot I need to annotate the common mutated genes within the clusters... how can i do that ??

Thank you in advance,

Answer 1

[Chris Miller]

1) Generally, CNVs will be reported with start, stop, and amplitude. This may be log2 transformed ratio between tumor and normal, or reported as "absolute" copy number (1,2,3, etc) This is the value you need

2) To annotate commonly mutated genes, see the positionsToHighlight argument to plot.2d. It takes a list of coordinates (chr/pos) matching up with your sites in the first two cols (sites to highlight) and then a label in the third - add the highlightsHaveNames=TRUE param.