R: Create a repertoire of public clonotypes

pubRep {immunarch} | R Documentation

## Create a repertoire of public clonotypes

### Description

Create a repertoire of public clonotypes

### Usage

    pubRep(
      .data,
      .col = "aa+v",
      .quant = c("count", "prop"),
      .coding = TRUE,
      .min.samples = 1,
      .max.samples = NA,
      .verbose = TRUE
    )

### 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.
`.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" to compute overlaps 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.
`.quant` | A string that specifies the column to be processed. Pass "count" to see public clonotype sharing with the number of clones, pass "prop" to see proportions.
`.coding` | Logical. If TRUE then preprocess the data to filter out non-coding sequences.
`.min.samples` | Integer. A minimal number of samples a clonotype must have to be included in the public repertoire table.
`.max.samples` | Integer. A maxminal number of samples a clonotype must have to be included in the public repertoire table. Pass NA (by default) to have the maximal amount of samples.
`.verbose` | Logical. If TRUE then output the progress.

### Value

Data table with columns for:

- Clonotypes (e.g., CDR3 sequence, or two columns for CDR3 sequence and V gene)

- Incidence of clonotypes

- Per-sample proportions or counts

### Examples

    # Subset the data to make the example faster to run
    immdata$data <- lapply(immdata$data, head, 2000)
    pr <- pubRep(immdata$data, .verbose=FALSE)
    vis(pr, "clonotypes", 1, 2)

[Package immunarch version 0.6.5 Index]