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AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
https://www.nature.com/articles/s41467-023-36790-9
GNU General Public License v3.0
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How to deal with EnsDb.Hsapiens.v86? #114

Closed autumnfe closed 3 months ago

autumnfe commented 3 months ago

When I ran SCEVAN, I encountered error.

So, I looked into the code of annotateGens function().

In the begining of code, I cound see the followin code:

if(organism == "human"){ edb <- EnsDB_Hsapiens_v86 #From EnsDb.Hsapiens.v86 }else{ edb <- EnsDb_Mmusculus_v79 #From EnsDb.Hsapiens.v86 }

Even if I load EnsDb.Hsapiens.v86 library, I couldn't see 'EnsDB_Hsapiens_v86' object. How to deal with this issue?

Also, when I see the code of preprocessMtx function(), I could see the following code:

if(organism == "human"){ totChr <- 22 cellcycle <- reactome_cellcycle #From EnsDb.Hsapiens.v86 }else{ totChr <- 19 cellcycle <- reactome_cellcycle_Mmusculus #From EnsDb.Hsapiens.v86 }

But, I couldn't find 'reactome_cellcycle' object at all. How to resolve this issue?

AntonioDeFalco commented 3 months ago

They are objects stored within the R package, which you can find in the sysdata.rda of the R folder.