countFastaKmers: countFastaKmers function: Counts DNA k-mers from (compressed)...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Details Value Note Author(s) References Examples

Reads (compressed) fasta files and counts for DNA k-mers in the sequence.

1	countFastaKmers(filenames,k=4)

`filenames`	`character`: Vector of fasta file names. Files can be gz compressed.
`k`	Length of counted DNA k-mers.

Maximal allowed value for k is 12.

matrix.

The static size of the retured k-mer array is 4^k.

Wolfgang Kaisers

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-177

basedir <- system.file("extdata", package="seqTools")
filename <- file.path(basedir,"small.fa")
## Not run: writeFai(filename, "small.fa.fai")
res <- countFastaKmers(filename, k=2)