R: Analysis immune repertoire kmer statistics: sequence...

split_to_kmers {immunarch} | R Documentation

## Analysis immune repertoire kmer statistics: sequence profiles, etc.

### Description

Analysis immune repertoire kmer statistics: sequence profiles, etc.

### Usage

    split_to_kmers(.data, .k)

    kmer_profile(.data, .method = c("freq", "prob", "wei", "self"), .remove.stop = TRUE)

### Arguments

`.data` | Character vector or the output from `getKmers`.
`.k` | Integer. Size of kmers.
`.method` | Character vector of length one. If "freq" then return a position frequency matrix (PFM) - a matrix with occurences of each amino acid in each position. If "prob" then return a position probability matrix (PPM) - a matrix with probabilities of occurences of each amino acid in each position. This is a traditional representation of sequence motifs. If "wei" then return a position weight matrix (PWM) - a matrix with log likelihoods of PPM elements. If "self" then return a matrix with self-information of elements in PWM. For more information see https://en.wikipedia.org/wiki/Position_weight_matrix.
`.remove.stop` | Logical. If TRUE (by default) remove stop codons.

### Value

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

`kmer_profile` - a matrix with per-position amino acid statistics.

### Examples

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

[Package immunarch version 0.6.7 Index]