saving the scRepertoire object

[Chiranjit1504]

I was wondering how I save the scRepertoire object after I have used combineTCR function on my list.

Donor.TCR <- combineTCR(contig_list,
samples = c("DL","DL","DL","DL","DLN","DLN","DLN","DLN"), # combineExpression
ID = c("6414", "6442", "6446", "7678", "6414", "6442","6446","7678"))

I tried saving the Donor.TCR as a Rdata object but whenever I load the object back, I cannot access it in the way I would for a scRepertoire object.

[ncborcherding]

Hey @Chiranjit1504,

I would look at how you are saving and retrieving the rda file - there should be not issue with this from the scRepertoire perspective. Here is a reproducible example (I just ensured this works as well):

library(scRepertoire)
data("contig_list") 
combined.TCR <- combineTCR(contig_list, 
                           samples = c("P17B", "P17L", "P18B", "P18L", 
                                       "P19B","P19L", "P20B", "P20L"))
save(combined.TCR, file = "~/Combined.TCR.rda")   
load("~/Combined.TCR.rda")  

Hope that helps,
Nick

[Chiranjit1504]

Hi Nick, Thank you so much for the reply. When I am loading it back in my script, I am only able to get its name back in the environment but not the object. Is there something I am missing? PFA screenshot below. Chiranjit

…

On Fri, Feb 7, 2025 at 9:11 PM theHumanBorch ***@***.***> wrote: Hey @Chiranjit1504 <https://github.com/Chiranjit1504>, I would look at how you are saving and retrieving the rda file - there should be not issue with this from the scRepertoire perspective. Here is a reproducible example (I just ensured this works as well): library(scRepertoire) data("contig_list") combined.TCR <- combineTCR(contig_list, samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L")) save(combined.TCR, file = "~/Combined.TCR.rda") load("~/Combined.TCR.rda") Hope that helps, Nick — Reply to this email directly, view it on GitHub <#474 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BKI2CYTJ3IH7JZF4Z3YW4AD2OUOOVAVCNFSM6AAAAABWVYCUZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNBUGEZTKMJUGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>