countKmersCertain: Get the Kmer Counts for certainty nucleotides (ie remove...

In mathornton01/Genomic-DFT-Yin-R: Fourier Analysis for Genomic Signals

Description

Produces a vector of the counts of all of the kmers in a particular character string representing a genetic sequence. This implementation will first replace all non-ACGT components with a gapping place holder (-) and will then proceed to count all mers present which do not contain any gaps.

Usage

countKmersCertain(genomicString, k, freq = FALSE)

Arguments

genomicString	A genomic string in the character string format in R
k	The size of the kmers which the user would like to produce a count matrix for
freq	Return the relative proportions of kmers of that kind (default FALSE - return raw counts)

Value

A vector of kmer counts that contains counts for the kmers in lexicographical ordering.

Examples

countKmersCertain(sarscvmay[1,]$sequences,5)

mathornton01/Genomic-DFT-Yin-R documentation built on Dec. 21, 2021, 2:52 p.m.