countFastaKmers: countFastaKmers function: Counts DNA k-mers from (compressed)...

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

View source: R/fastaFunctions.R

Description

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

Usage

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countFastaKmers(filenames,k=4)

Arguments

filenames

character: Vector of fasta file names. Files can be gz compressed.

k

Length of counted DNA k-mers.

Details

Maximal allowed value for k is 12.

Value

matrix.

Note

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

Author(s)

Wolfgang Kaisers

References

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

Examples

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

seqTools documentation built on Nov. 8, 2020, 5:20 p.m.