Incomplete merging of vdj data and seurat with combineExpression function

[cnwokolo24]

Hi Nick,

Thank you for this very helpful tool.
I am trying to combine tcr & bcr data to my seurat object which has multiple samples integrated.
But after adding the list(tcr, bcr) of all the samples, I have to format the barcode to match my seurat object and when I do this only the first sample merges with the seurat obj.
Please see my code below to see what I am doing wrong.

##VDJ data
tcr_list = list(AIG1_TCR, AIG2_TCR, AIG3_TCR, AIG4_TCR, AIG5_TCR, HC1_TCR, HC2_TCR, HC3_TCR)
bcr_list = list(AIG1_BCR, AIG2_BCR, AIG3_BCR, AIG4_BCR, AIG5_BCR, HC1_BCR, HC2_BCR, HC3_BCR)

#combine
combined_tcr = combineTCR(tcr_list, samples = c("AIG1", "AIG2", "AIG3", "AIG4", "AIG5", "HC1", "HC2", "HC3"),
removeNA = T)
combined_bcr <- combineBCR(bcr_list, samples = c("AIG1", "AIG2", "AIG3", "AIG4", "AIG5", "HC1", "HC2", "HC3"),
removeNA = T, threshold = 0.85)

##add variable
combined_tcr <- addVariable(combined_tcr,
name = "condition",
variables = c("AIG", "AIG", "AIG", "AIG", "AIG", "HC", "HC", "HC"))
combined_bcr <- addVariable(combined_bcr,
name = "condition",
variables = c("AIG", "AIG", "AIG", "AIG", "AIG", "HC", "HC", "HC"))
list.receptors <- c(combined_tcr, combined_bcr)

#format list.receptors to match seurat object
list.receptors[["AIG1"]][["barcode"]] <- paste0(sub("^AIG1_", "", list.receptors[["AIG1"]][["barcode"]]), "1")
list.receptors[["AIG2"]][["barcode"]] <- paste0(sub("^AIG2", "", list.receptors[["AIG2"]][["barcode"]]), "1")
list.receptors[["AIG3"]][["barcode"]] <- paste0(sub("^AIG3", "", list.receptors[["AIG3"]][["barcode"]]), "1")
list.receptors[["AIG4"]][["barcode"]] <- paste0(sub("^AIG4", "", list.receptors[["AIG4"]][["barcode"]]), "1")
list.receptors[["AIG5"]][["barcode"]] <- paste0(sub("^AIG5", "", list.receptors[["AIG5"]][["barcode"]]), "_1")

list.receptors[["HC1"]][["barcode"]] <- paste0(sub("^HC1_", "", list.receptors[["HC1"]][["barcode"]]), "1")
list.receptors[["HC2"]][["barcode"]] <- paste0(sub("^HC2", "", list.receptors[["HC2"]][["barcode"]]), "1")
list.receptors[["HC3"]][["barcode"]] <- paste0(sub("^HC3", "", list.receptors[["HC3"]][["barcode"]]), "_1")

##add vdj to seurat to subsetted tcells with raw values
data.combined.vdj <- combineExpression(list.receptors,
data.combined,
cloneCall="gene",
group.by = "sample",
addLabel = T, proportion = F)

And when I run I see only one AIG
clonalProportion(tcells.vdj,

•              split = c(10, 100, 1000, 10000, 30000, 1e+05),
  

•              split.by = "condition", 
  

•              cloneCall = "nt",
  

•              chain = "both",
  

•              exportTable = T)
  

  [1:10] [11:100] [101:1000] [1001:10000] [10001:30000] [30001:1e+05]
  AIG 10 71 0 0 0 0

When I run it combineExpression without formating the list.receptors, I get this: ""Error in [[<-:
! Cannot add more or less meta data without cell names
Run rlang::last_trace() to see where the error occurred.
Warning message:
In combineExpression(list.receptors, tcells, cloneCall = "gene", :
< 1% of barcodes match: Ensure the barcodes in
the Seurat object match the
barcodes in the combined immune receptor list from
scRepertoire - most common issue is the addition of the
prefixes corresponding to samples and 'ID' in the combineTCR/BCR()
functions"""
Please advise.

[ertingtang]

Hi! I wonder how you resolved this issue eventually? I encountered the same issue. Thanks for your reply in advance!