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Miaoyx323 / stCancer

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infercnv results #6

Closed pratapstat closed 2 years ago

pratapstat commented 2 years ago

Hi, After running the stCancer package, infercnv was done successfully and cnv heatmap was generated but don't have access to text files results even though in the package there are lines of code were there in package to generate txt files results.

Screenshot 2022-07-28 at 3 08 35 PM

Screenshot 2022-07-28 at 3 13 00 PM

pratapstat commented 2 years ago

Hi,

Could i know update regarding this ?

Best Regards, Pratap

Miaoyx323 commented 2 years ago

Hi,

According to the pictures you provided, you used default copyKAT function to analyze CNV and it will not generate the above txt files. You can set CNV.analysis.func of the stAnnotation function to "inferCNV" and provide the reference data of normal tissues to get the results calculated through inferCNV, by which you can get txt files.

We recommend that you use the current default copykat method, which dose not require reference data. The principle of copykat method can be found in this paper, Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes.

Best, Miao

pratapstat commented 2 years ago

Thanks for providing the info and the reference paper.

Best Regards, Pratap