R: Select specific clonotypes using barcodes from single-cell...

select_barcodes {immunarch} | R Documentation

## Select specific clonotypes using barcodes from single-cell metadata

### Description

Subset the input immune repertoire by barcodes. Pass a vector of barcodes to subset or a vector cluster IDs and corresponding barcodes to get a list of immune repertoires corresponding to cluster IDs. Columns with clonotype counts and proportions are changed accordingly to the filtered barcodes.

### Usage

    select_barcodes(.data, .barcodes, .force.list = FALSE)

### Arguments

`.data` | The data to be processed. Can be data.frame, data.table, or a list of these objects. Every object must have columns in the immunarch compatible format. immunarch_data_format Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects. Note: each connection must represent a separate repertoire.
`.barcodes` | Either a character vector with barcodes or a named character/factor vector with barcodes as names and cluster IDs a vector elements. The output of Seurat's `Idents` function works.
`.force.list` | Logical. If TRUE then always return a list, even if the result is one data frame.

### Value

An immune repertoire (if ".barcodes" is a barcode vector) or a list of immune repertoires (if ".barcodes" is named vector or an output from Seurat::Idents()). Each element is an immune repertoire with clonotype barcodes corresponding to the input barcodes. The output list's names are cluster names in the ".barcode" argument (Seurat::Idents() case only).

### See Also

select_clusters

### Examples

    ## Not run:
    data(immdata)
    # Create a fake single-cell data
    df <- immdata$data[[1]]
    df$Barcode <- "AAAAACCCCC"
    df$Barcode[51:nrow(df)] <- "GGGGGCCCCC"
    barcodes <- "AAAAACCCCC"
    df <- select_barcodes(df, barcodes)
    nrow(df)

    ## End(Not run)

[Package immunarch version 0.6.7 Index]