R: countGenomeKmers: Counting K-mers in DNA sequences.
countGenomeKmers
R Documentation
countGenomeKmers: Counting K-mers in DNA sequences.
Description
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.
character. Vector of DNA sequences. 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.
seqid
numeric. Vector of (1-based) values describing the
index of the analyzed sequences inside the given dna vector.
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!)
Details
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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/countGenomeKmers.Rd_%03d_medium.png", width=480, height=480)
> ### Name: countGenomeKmers
> ### Title: countGenomeKmers: Counting K-mers in DNA sequences.
> ### Aliases: countGenomeKmers
> ### Keywords: countGenomeKmers
>
> ### ** Examples
>
> 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)
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
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.