Hi, I have a concept question on the recent seg2gsm.py file and CNV data. I am not clear on the modification that allows extended features in the segmentation gsm. So how many features can be expected from core and then the extended features? How does this impact classification? Is it possible to access this list of features?
Upon running the most recent script, seg2gsm generates 74 features for my data. Keeping all other files from a Summer 2025 run fixed, my classifications have changed and the seg2gsm files look different from the original across all samples. I am trying to understand what update is doing and are these large enough shifts to reorganize classification subtypes? Any further information on effect of copy number on this tool would be great. Thanks!
Hi, I have a concept question on the recent seg2gsm.py file and CNV data. I am not clear on the modification that allows extended features in the segmentation gsm. So how many features can be expected from core and then the extended features? How does this impact classification? Is it possible to access this list of features?
Upon running the most recent script, seg2gsm generates 74 features for my data. Keeping all other files from a Summer 2025 run fixed, my classifications have changed and the seg2gsm files look different from the original across all samples. I am trying to understand what update is doing and are these large enough shifts to reorganize classification subtypes? Any further information on effect of copy number on this tool would be great. Thanks!