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navinlabcode / copykat

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Output files are written to working directory #116

Open rVMLql58 opened 2 months ago

rVMLql58 commented 2 months ago

When running copykat it generates multiple files that are written to the current working directory. These include an .rds file with clustering results, text files with cna results and predictions, and a clustering heatmap. When iterating over multiple samples this generates a large number of files.

Could you update copykat so that users can supply a path where these files will be written? Also, can users have the option to suppress some outputs? I tried setting the 'plot.genes' parameter to FALSE which should suppress heatmap plotting but the JPEG file is still being generated.

23ycjiang commented 1 week ago

Hello, have you found WES ground truth data and gene location information data matching the data in the article?

rVMLql58 commented 1 week ago

@23ycjiang - how does your comment relate to the issue I opened (changing flie output settings)?

23ycjiang commented 1 week ago

Hello, I'm very sorry that this question has been bothering me for a long time, so I would like to ask others. Because the evaluation index of the last method in the article requires this supporting data, I only found scRNA, do you have any matching data? We look forward to hearing from you. Thank you so much.