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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Adding GEX to VGM created with AIRR_to_VGM #47

Open kbruton opened 1 year ago

kbruton commented 1 year ago

Hi there. I used PlatypusDB_AIRR_to_VGM to convert a TRUST4 airr.tsv output to a VGM object. As expected, this object now contains the VDJ data in VGM[[1]] and empty GEX data in VGM[[2]].

I am wondering how I can now integrate GEX data from an existing Seurat object to the VGM produced by PlatypusDB_AIRR_to_VGM.

Any suggestions would be greatly appreciated!

vickreiner commented 1 year ago

Hi,

you can add the GEX to the VGM object and then run VGM_integrate as such: VGM[["GEX"]] <- your_Seurat_object VGM <- VGM_integrate(VGM) Please note, that the GEX file does need a sample_id and group_id column to be mapped correctly. Please also ensure, that the barcodes in GEX (colnames(GEX)) are not formatted differently than VGM[["VDJ"]]$barcode column.

Let me know if you have any further questions!