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data2intelligence / SpaCET

Spatial Cellular Estimator for Tumors
GNU General Public License v3.0
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SpaCET with other species? And GeneSetScore does not work in Win OS. #29

Open rln0005 opened 5 months ago

rln0005 commented 5 months ago

First off, THANK YOU to SpaCET team for creating such a useful and easy-to-use tool for spatial cancer research! It has been very valuable in our research. My question is if it can be used for tumors from other species that serve as models for the human disease (ie, canine)? Is the CNV analysis specific to gene names, or their coordinates on the chromosome? If it's the former, I would think it would be fine to use with model species.

Thanks in advance!

beibeiru commented 5 months ago

Hi, Rebecca,

We are extremely glad that our tool can help you in your research.

Q: My question is if it can be used for tumors from other species that serve as models for human disease (ie, canine). A: The gene pattern dictionaries (e.g., CNV) in SpaCET source from the human species. We have not evaluated them for non-human species.

Q: Is the CNV analysis specific to gene names, or their coordinates on the chromosome? A: Yes, the CNV signature is gene symbol-based. To your knowledge, if you think the CNV pattern is similar between humans and the model species of interest, you could apply SpaCET to your sample. I recommend that you compare the region of inferred malignant cells with H&E images to evaluate the deconvolution results. Look forward to your feedback.

Best, Beibei

rln0005 commented 5 months ago

Hi Beibei,

Thank you so much for your quick and helpful response. The results with canine are looking good so far.

I have one additional question - I am trying to follow the Gene Set Score Calculation Vignette, but I keep encountering the same error.

SpaCET_obj <- SpaCET.GeneSetScore(SpaCET_obj, GeneSets="Hallmark") Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file 'C:/Users/rln0005/AppData/Local/R/win-library/4.3/SpaCET/extdata/GeneSetsHallmark.gmt': No such file or directory

None of the other gene sets (ie, TLS, cancer cell state) work either. Do you have any advice for this error? Thank you.

beibeiru commented 5 months ago

Hi, Rebecca,

Thank you for reporting this bug to me. It is caused by the difference in trailing path separators between Win and Linux. I will fix it soon.

However, you still can follow the two steps below to run Gene Set Score Calculation before I update our software.

Step1: Download the gmt file to your local computer from https://github.com/data2intelligence/SpaCET/tree/main/inst/extdata/GeneSets

Step2: Run

gmt <- read.gmt("Path_to_gmt_file")
SpaCET_obj <- SpaCET.GeneSetScore(SpaCET_obj, GeneSets = gmt)

If you want to try other gene sets, please follow this part. https://data2intelligence.github.io/SpaCET/articles/GeneSetScore.html#calculate-other-gene-sets-score

Please let me know if it does not work for you.

Best, Beibei

rln0005 commented 5 months ago

Thank you so much!! It worked :)

Best, Rebecca