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Can I integrate data with iCellR? #27
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Yes, it is very easy. First read each patient data like this:
Then use the Example for 3 patients: Then make an object:
CPCA is for batch alignment, which you run instead of PCA step if you wish to do batch alignment. |
Thank you for the quick reply. The CPCA can work for the batch effect,right? If it is, how can I use it to my data . Like the "my.obj <- iba(my.obj,dims = 1:30, k = 10,ba.method = "CPCA", method = "gene.model", gene.list = my.obj@gene.model)" change the gene.model to orig.ident (sorry , I use the seurat)? OR if not, how can I integrate the data to aviod the batch effect. |
Yes, you can replace |
Thank you very much! |
I appreciate this great tools for analysis. Could I ask you that there is a integration function for multiple data or not.
I have about 50 patients data (all are the 10x files) which I want to merge them into one object. I find the "Combined Principal Component Alignment (CPCA)". But how can I use for my data. Thank you very much.
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