Adding gene annotation to CNAmatrix + p and q information

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
20/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
data

Research direction

Start with the documentation's Step 5 and the reported CNAmatrix, full.anno, tumor.cells, and tumor.matrix objects. Reproduce the row-count and identifier mismatches before investigating the requested gene annotation and p/q chromosome plotting. Done means the three questions have documented, reproducible guidance or a clearly scoped implementation path.

Written by the indexing model from the issue text.

Description

Hello, thanks for this tool.
I have a couple of questions and I would appreciate some guidance on how to move forward.

(1) I ran one sample in CopyKat. The output CNAmatrix looks something like this:
Screenshot 2023-09-04 at 11 56 22
I have been trying to add gene symbols to the matrix, in order to plot some relevant genes. However, I haven't been able to do that. I am using full.anno (annotation table supplemented by the package).

I first tried to do cbind(CNA.test, full.anno), but I get the following error:
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 12167, 56051

So I tried to subset the full.anno matrix to only have the abspos valuess found in my CNA.test matrix. I tried it in different ways and none worked (i get an empty matrix):
Screenshot 2023-09-04 at 12 02 30

I then extracted one of the abspos of the CNA.test, and looked for it in full.anno matrix and I couldn't find it. So it seems like I am unable to match full.anno$abspos with CNA.test$abspos. Is there a way around this? Am I missing a step?

(2) I am following the downstream analysis for tumor cells clustering as shared in the documentation (Step 5: define subpopulations of aneuploid tumor cells). I am able to subset tumor cell names (tumor.cells, length(tumor.cells) is 6992). My issue is that when I subset for the tumor.matrix, I only get 8 cells instead of my original 6992 cells. Can you please help me through this?

(3) Is there a way I can add q and p information to the plot? Split each chromosome panel to either p or q. If not, what are ways you suggest I can quantify those copy number alterations, especially in single-cell?

Your help would be greatly appreciated.
Best,
Raghad

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