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Associating VDJ clonotyping data with scRNA-seq in Seurat
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11 months ago
jared.andrews07 ♦ 2.4k
St. Louis, MO

Single cell technologies are booming, but figuring out how to integrate multimodal data sets is certainly still a challenge, even with well-supported and constantly updated software (like Seurat). I struggled to find any info as to how to associate my Chromium 10X TCR-sequencing data with the corresponding scRNA-seq data. Seurat has a fairly good vignette on associating multimodal data, but that approach doesn't really work for V(D)J cell profiling.

The author's commented that the way to do it was by adding to the metadata of a Seurat object, but the method to do that remained unclear (partially due to the AddMetaData function not having great documentation). In reality, it's pretty easy - you can add any dataframe as Metadata to a Seurat object so long as its row names match the objects as shown with object@meta.data.

The VDJ info from 10X takes some amount of fanagling to get in a proper data frame with 1 row per cell with usable clonotype info. This R function makes it straightforward for a typical CellRanger3 workflow used for both scRNA and TCR-seq and Seurat v3:

add_clonotype <- function(tcr_location, seurat_obj){
    tcr <- read.csv(paste(tcr_folder,"filtered_contig_annotations.csv", sep=""))

    # Remove the -1 at the end of each barcode.
    # Subsets so only the first line of each barcode is kept,
    # as each entry for given barcode will have same clonotype.
    tcr$barcode <- gsub("-1", "", tcr$barcode)
    tcr <- tcr[!duplicated(tcr$barcode), ]

    # Only keep the barcode and clonotype columns. 
    # We'll get additional clonotype info from the clonotype table.
    tcr <- tcr[,c("barcode", "raw_clonotype_id")]
    names(tcr)[names(tcr) == "raw_clonotype_id"] <- "clonotype_id"

    # Clonotype-centric info.
    clono <- read.csv(paste(tcr_folder,"clonotypes.csv", sep=""))

    # Slap the AA sequences onto our original table by clonotype_id.
    tcr <- merge(tcr, clono[, c("clonotype_id", "cdr3s_aa")])

    # Reorder so barcodes are first column and set them as rownames.
    tcr <- tcr[, c(2,1,3)]
    rownames(tcr) <- tcr[,1]
    tcr[,1] <- NULL

    # Add to the Seurat object's metadata.
    clono_seurat <- AddMetaData(object=seurat_obj, metadata=tcr)
    return(clono_seurat)
    }

This saves a clonotype ID and CDR3 AA sequence, as the clonotype ID may not be usable as an identifier if samples are combined.

Hopefully this saves someone a bit of time.

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Since you had some confusion about AddMetaData, I just wanted to add that object@meta.data is just a data frame. If you are more comfortable with standard R data frames, you can do something like

object@meta.data$new_col <- some_values

or

object@meta.data[cell_barcodes, "new_col"] <- my_df[cell_barcodes, "some_col"]

to make sure that you are using the same cell barcodes for the labels.

Before v3, the AddMetaData function was actually relatively simple: https://github.com/satijalab/seurat/blob/65b77a9480281ef9ab1aa8816f7c781752092c18/R/interaction.R#L1120-L1137

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Thanks for the addition. Yeah, I actually went back to v2 to figure it out. I'm not quite sure why they changed the documentation to something that's (imo) more confusing, but you're dead-on that it's really simple once you realize it's just a data frame.

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