immunarch (version 0.6.4)

filter_barcodes: Filter clonotypes using barcodes from single-cell metadata

Description

Given the input data and a vector of barcodes, the function returns the input with cells which has at least one of the given barcode. Columns with clonotype counts and proportions are changed accordingly to the filtered barcodes.

Usage

filter_barcodes(.data, .barcodes)

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

Character vector. Vector of barcodes to use for filtering.

Value

An immune repertoire or a list of immune repertoires with clonotypes which have one or more barcodes in the input barcode vector and with clonotype abundances corrected.

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 <- filter_barcodes(df, barcodes)
nrow(df)
# }