Question about gisticChromPlot

Question

Question about gisticChromPlot

Closed this issue 8 months ago · 6 comments

Hello,

I have successfully ran GISTIC2 in canine data, and managed to get gisticChromPlot to generate a plot. However, the dog has 38 chromosomes, and the plot only shows the amplifications and deletions of the first 24 chromosomes (matching it to the human 23, X and Y chromosomes), meaning that I am missing data. So my question is: is there a way to make gisticChromPlot run with non-human data?

Thank you in advance and all the best.

Answer 1 · 2023-11-02T10:05:36.000Z

Hi,
Thanks for the issue. Unfortunately, the current implementation does not support non-human genomes. However, I don't see any problems with support for other organisms. It just needs the contig names and sizes.
Would it be possible to share the GISTIC object to test?

Answer 2 · 2023-11-02T13:55:12.000Z

Hello,

Thank you very much for the quick response. I am still a bit new to the world of bioinformatics so apologies for the silly question, but by "contig names and sizes" what do you mean? Also, here is a dummy GISTIC object file with canine CNA data. Hope this will help with running some tests.

Thank you again for all the help and best regards!

Answer 3 · 2023-11-06T14:06:57.000Z

Hi,

Thank you for sharing the data. Unfortunately, I spoke too early. It is a bit more complicated than I thought to support non-human genomes. I am swamped with work at the moment and it might take a while to look into this properly.

Answer 4 · 2024-01-15T02:10:04.000Z

This issue is stale because it has been open for 60 days with no activity.

Answer 5 · 2024-03-17T02:00:30.000Z

This issue is stale because it has been open for 60 days with no activity.

Answer 6 · 2024-03-31T02:03:22.000Z

This issue was closed because it has been inactive for 14 days since being marked as stale.