R: Calculate the kmer tatistics of immune repertoires

getKmers {immunarch} | R Documentation

## Calculate the kmer tatistics of immune repertoires

### Description

Calculate the kmer tatistics of immune repertoires

### Usage

    getKmers(.data, .k, .col = c("aa", "nt"), .coding = 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.
`.k` | Integer. Length of kmers.
`.col` | Character. Which column to use, pass "aa" (by default) for CDR3 amino acid sequence, pass "nt" for CDR3 nucleotide sequences.
`.coding` | Logical. If TRUE (by default) then remove all non-coding sequences from input data first.

### Value

Data frame with two columns (kmers and their counts).

### Examples

    data(immdata)
    kmers <- getKmers(immdata$data[[1]], 5)
    kmers %>% vis()

[Package immunarch version 0.6.5 Index]