Closed mbihie closed 11 months ago
Yes the code setup seems correct to me to compare two samples, if you reinstall SCEVAN I added the parameter listNormCells in the last commit https://github.com/AntonioDeFalco/SCEVAN/commit/285505291a538bbf93f743d8f7822e3812179858. Where you can pass normal cells as a list to be used as references added to the matrix:
listNormCells <- list(colnames(EP.MTX), colnames(EP.MTX))
results <- SCEVAN::multiSampleComparisonClonalCN( listCountMtx, listNormCells, analysisName = "all", organism = "human" ,
par_cores = 5 )
Let me know if it works. Regards
Hello,
I am trying to apply your tool, SCEVAN, to an integrated seurat object. I am trying to compare two types of tumors, and both are found in this seurat object (SeuratObject_TNBC.rds). I would need to use another seurat object to obtain the normal cells matrix as reference (SeuratObject_NormEpi.rds). I am not sure on how I can combine the two together for SCEVAN.
In the code below, I filtered the TNBC.rds object to two samples to compare different tumor types. I wanted to know how I could compare the two matrices. Would I add the normal counts matrix to both? Would I include all 3 in a list of matrices?
Here is the paper that explains the data in more detail (x).
Any help would be appreciated,