Thank you for the awesome tool!
I was wondering if its possible to ask scCancer to use the present Seurat object to perform some downstream analysis? For example, I want to use Seurat object to estimate the the malignant cells and non-malignant cells. Then I found that the “runMalignancy” should be a suitable function to estimate the malignant cells. However, I don't know how to prepared the “gene.manifest” and “cell.annotation” which were necessary for “runMalignancy” . After reaing the code in “runMalignancy”, I found that a “runCNV” function was used but I couldn't find the “runCNV” when I input the “？runCNV” in R. I wasn't able to solve this problem and I hope you can help me to perform the “runMalignancy”. Can you provide a example “gene.manifest” and “cell.annotation” data and the detail code of “runCNV” for me？
Thank you！
Chien-Fan
commented
6 months ago
Thank you for the awesome tool! I was wondering if its possible to ask scCancer to use the present Seurat object to perform some downstream analysis? For example, I want to use Seurat object to estimate the the malignant cells and non-malignant cells. Then I found that the “runMalignancy” should be a suitable function to estimate the malignant cells. However, I don't know how to prepared the “gene.manifest” and “cell.annotation” which were necessary for “runMalignancy” . After reaing the code in “runMalignancy”, I found that a “runCNV” function was used but I couldn't find the “runCNV” when I input the “？runCNV” in R. I wasn't able to solve this problem and I hope you can help me to perform the “runMalignancy”. Can you provide a example “gene.manifest” and “cell.annotation” data and the detail code of “runCNV” for me？ Thank you！