Select specific clonotypes using barcodes from single-cell metadata

Subsets the input immune repertoire by barcodes. Creates 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::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, 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 returns 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 names are cluster names in the ".barcode" argument (Seurat::Idents() case only).

See also

select_clusters

Examples

# \dontrun{
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)
#> Error in setnames(df, "", "Barcode"): Items of 'old' not found in column names: []. Consider skip_absent=TRUE.
nrow(df)
#> [1] 6532
# }