sciClone annotation help

Question

[js2dark]

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

Answer 1

[Chris Miller]

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 '[e-mail]' (where sco is the object returned from the sciClone function) and the R merge function should help)

[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.