countFastaKmers {seqTools} | R Documentation |
Reads (compressed) fasta files and counts for DNA k-mers in the sequence.
countFastaKmers(filenames,k=4)
filenames |
|
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)