R: Immune repertoire spectratyping

spectratype {immunarch} | R Documentation

## 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. Pass "id" to count every clonotype once. Pass "count" to take into the account number of clones per clonotype.
`.col` | A string that specifies the column(s) to be processed. Pass 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)

[Package immunarch version 0.6.5 Index]