Entering edit mode
11 months ago
JULIA HELENA
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0
Hi!
I'm learning new skills on Rstudio and maftools for my final paper in graduation. I'm analyzing some genes of my samples (thyroid cancer samples, submitted to RNAseq) and now I'm working on the maf files in R and using the maftools package. I used the command co-oncoplot (because I have 2 groups, disease-free and stable disease) and I get the genes that were commonly mutated in both groups, but now I would like to know which genes are different between the two groups.
I'm not familiar yet with the functions that the maftools package can offer, so I hope I'm not asking something super easy and dumb, but this is a real question that I'm struggling with.
Thanks!
If this is the coOncoplot you're referring to, you might be able to give it the list of genes you're interested in and have it plot them.
Yes, this is the one!
I already managed to get the top genes that are mutated in both of my groups, and also get the coOncoplot for the genes that I chose. but, I am trying to see the genes that are not mutated in both of my groups, i. e. I would like to see the ones that are exclusive for one group or another.
It doesn't have to be an coOoncoplot, since I understand that this command is the opposite of what I'm trying to do, but I was wondering if maftools has some graphic example that is as didactic as the coOncoplot for this thing that I'm trying to do.
Thank you for your help, means a lot to me!
I don't have any other visualization tool to recommend to you (I don't visualize mutations much) but I do have a question for you - were you able to extract list of exclusive mutations? That would be the first step in testing if coOncoplot can handle subset-exclusive mutations.