start
and width
parameter.
From each position of the search window, a DNA k-mer is identified
on the right hand side on the given DNA sequence.
Each value in the start
vector defines the left border
of a search window.
The size of the search window is given by the appropriate value in the
width
vector.
The function is intended to count DNA k-mers in selected regions (e.g. exons)
on DNA sequence.
countDnaKmers(dna,k,start,width)
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 current DNA k-mer is skipped.numeric
. Number of nucleotides in tabled DNA motifs.numeric
. Vector of (1-based) start positions for
reading frames.
Reading frame is counted to the right side of the DNA string.numeric
. Defines 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.nchar(dna)-k+1
.
The function throws the error 'Search region exceeds string end'
when a value start + width + k > nchar(dna) + 2
occurs.seq <- "ATAAATA"
countDnaKmers(seq, 2, 1:3, 3)
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