revCountDnaKmers: revCountDnaKmers: Counting K-mers in DNA sequence.

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description

Counts DNA K-mers for reverse complement of given DNA sequence. The k-mers are counted in a set of search windows, which are defined by start and width parameter. From each position of the search window, a DNA k-mer is identified on the left hand side on the reverse complement of the given DNA sequence. Each value in the start vector defines the right border of a search window. The size of the search window is given by the appropriate value in the width vector.

Usage

revCountDnaKmers(dna, k ,start, width)

Arguments

dna	character. Single DNA sequence (vector of length 1). dna must not contain other characters than "ATCGN". Capitalization does not matter. When a 'N' character is found, the ongoing identification of a DNA k-mer is terminated.

k	numeric. Number of nucleotides in tabled DNA motifs.

start

numeric. Vector of (1-based) start positions for reading frames.

width

numeric. Defines number of k-mers (size of search window) for each start position. Must have the same length as start or length 1 (in which case the values of width are recycled.)

Details

The start positions for identification of DNA k-mers are all positions in {start-width+1,...,start}. In order to prevent counting before the first nucleotide of the DNA sequence, all start values must be >= width + k. The function throws an error when this border is exceeded.

Value

matrix. Each colum contains the motif-count values for one frame. Each row represents one DNA motif. The DNA sequence of the DNA motif is given as row.name.

Author(s)

Wolfgang Kaisers

Examples

rseq <- "TATTAT"
revCountDnaKmers(rseq, 2,6:4, 2)

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.