I'm using sciClone package in R for assessing the clonality and subclonality of my tumor samples. I get the results including 2d and 3d clusters and the table. Also, I added the annotation list which is made up of 3-columns: 1) chromosome 2) start position 3) gene name for my output table as well. I expected to see chromosome, position, and gene name in my output table but I only see the chromosome and position. Is there something I can do so that the output table would include the gene names of the mutations as well? Thank you
Right now, the annotation file is only used to label points on the plots. It's pretty straightforward to intersect the clustering output with your gene list post-hoc, though. (Or to do it in R, for that matter - the cluster list is stored in 'sco@vafs.merged' (where sco is the object returned from the sciClone function) and the R merge function should help)
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Chris Miller
I should also mention that I'm happy to accept pull requests on the github repo if you do hack in a solution that adds annotations to the cluster file.
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