fastqKmerLocs {seqTools} | R Documentation |
Reads (compressed) FASTQ files and counts for DNA k-mers for each position in sequence.
fastqKmerLocs(filenames, k=4)
filenames |
Vector of FASTQ file names. Files can be gz compressed. |
k |
Length of counted DNA k-mers. |
Maximal allowed value for k is 12.
list
. The length of the list equals the number of given
filenames.
Contains for each given file a matrix with 4^k rows and
(maxSeqLen - k + 1) columns (maxSeqLen= maximum read length).
The matrix contains for each k-mer and
k-mer-start position the counted values.
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 1767-1771
basedir <- system.file("extdata", package="seqTools") setwd(basedir) res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2) res <- fastqKmerLocs("test_l10_atcg.fq", k=2) res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2) res <- fastqKmerLocs("test_l6_multi_line.fq", k=2)