kmer_counter_wrapper: Represents the kmers present in the input with their integer...

In TomMayo/kmermods: Represents Kmers As Integers Along The Genome

Description

This runs over the input calculating the integer value for every kmer that begins at that location. It returns the resutls as a vector. It acts as a wrapper to kmer_counter, and takes in DNAStringSet objects from the Biostrings package (available from Bioconductor)

Usage

kmer_counter_wrapper(dna_input, chunk_size, alph, k)

Arguments

dna_input	The DNA sequence, as a DNAStringSet object (see Biostrings package)
chunk_size	The length of DNA to send in each chunk for parallel processing by kmer_counter
alph	The alphabet we are using. A dataframe created using build_alphabet()
k	The length of kmers we are assessing. Used as a check.

Value

An integer vector corresponding to the kmers at each starting point in the DNA

Author(s)

Tom Mayo [e-mail]

Examples

data(dna_input)
alph <- kmermods::build_alphabet()
kmer_counter_wrapper(dna_input,100,alph,4)

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