spectratype {immunarch}

Immune repertoire spectratyping

Description

Immune repertoire spectratyping

Usage

spectratype(.data, .quant = c("id", "count"), .col = "nt")

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.

.quant

Select the column with clonal counts to evaluate. Set to "id" to count every clonotype once. Set to "count" to take into the account number of clones per clonotype.

.col

A string that specifies the column(s) to be processed. The output is one of the following strings, separated by the plus sign: "nt" for nucleotide sequences, "aa" for amino acid sequences, "v" for V gene segments, "j" for J gene segments. E.g., pass "aa+v" for spectratyping on CDR3 amino acid sequences paired with V gene segments, i.e., in this case a unique clonotype is a pair of CDR3 amino acid and V gene segment. Clonal counts of equal clonotypes will be summed up.

Value

Data frame with distributions of clonotypes per CDR3 length.

Examples

# Load the data
data(immdata)
sp <- spectratype(immdata$data[[1]], .col = "aa+v")
vis(sp)