unwrap_kmers_vect: Takes in a single long kmer, for example a 26mer, and returns...

Description Usage Arguments Value Author(s)

Description

Takes in a single long kmer, for example a 26mer, and returns the composite shorter kmers for some k, for example, all the 10mers within the 26mer. It is designed to be used to unwrap a dense representation of the kmers: for example, given the 26mers every 19 base pairs, we can quickly extract all 8mers.

Usage

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unwrap_kmers_vect(kmers, old_len = 26, new_len = 8, base = 4,
  num_kmers = 0L)

Arguments

old_len

The length of the kmer represented by kmer (ie k)

new_len

The length of the kmers we want to extract, eg, if we want 8mers, new_len = 8

base

The length of the alphabet. For normal DNA sequence this is 4.

num_kmers

The number of the new kmers to return. The functions returns the first num_kmers in the vector. Default value is 0, which returns all kmers.

kmer

A number representing a single large kmer, with k = old_len

Value

A vector of doubles (actually integers represented as doubles), representing all the (new_len)-mers contained within the single (old_len)-mer.

Author(s)

Tom Mayo t.mayo@ed.ac.uk


TomMayo/kmermods documentation built on May 9, 2019, 4:53 p.m.