countGenomeKmers: countGenomeKmers: Counting K-mers in DNA sequences.
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description Usage Arguments Details Value Author(s) Examples

Counts K-mers of DNA sequences inside fasta files. 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.

1	countGenomeKmers(dna,seqid,start,width,strand,k)

`dna`	`character`. Vector of DNA sequences. `dna` must not contain other characters as "ATCGN". Capitalization does not matter. When a 'N' character is found, the current DNA k-mer is skipped.
`seqid`	`numeric`. Vector of (1-based) values describing the index of the analyzed sequences inside the fasta file.
`start`	`numeric`. Vector of (1-based) start positions for reading windows.
`width`	`numeric`. Vector of window width values.
`strand`	`factor or numeric`. First factor level (or numeric: 1) value will be interpreted as (+)-strand. For any other values, the reversed complement sequence will be counted (in left direction from start value).
`k`	`numeric`. Number of nucleotides in tabled DNA motifs. Only a single value is allowed (length(n)=1!)

The function returns a matrix. Each colum containts 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)

Loading required package: zlibbioc
   1 2
AA 0 0
AC 0 0
AG 0 0
AT 0 0
CA 0 0
CC 3 0
CG 1 0
CT 0 0
GA 0 0
GC 0 0
GG 0 0
GT 0 0
TA 0 0
TC 0 1
TG 0 0
TT 0 3