countGenomeKmers {seqTools} | R Documentation |
Counts K-mers of DNA sequences inside a vector of DNA sequences.
The k-mers are searched 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 right hand side on the given DNA sequence.
Each value in the start
vector defindes 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 chromosomes while respecting strand orientation.
countGenomeKmers(dna, seqid, start, width, strand, k)
dna |
|
seqid |
|
start |
|
width |
|
strand |
|
k |
|
The function returns a 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.
matrix
.
Wolfgang Kaisers
sq <- "TTTTTCCCCGGGGAAAA" seqid <- as.integer(c(1, 1)) start <- as.integer(c(6, 14)) width <- as.integer(c(4, 4)) strand <- as.integer(c(1, 0)) k <- 2 countGenomeKmers(sq, seqid, start, width, strand, k)