seqTools (version 1.6.0)

fastqKmerSubsetLocs: fastqKmerSubsetLocs function: Counts for a given DNA k-mer subset position wise from FASTQ files.

Description

Reads (compressed) FASTQ files and counts for given DNA k-mer subset for each position in sequence. The k-mer subset is given by a vector of k-mer indices. k-mer indices can be obtained from DNA k-mers with the function kMerIndex.

Usage

fastqKmerSubsetLocs(filenames, k=4, kIndex)

Arguments

filenames

character. Vector of fastqKmerSubsetLocs file names. Files can be gz compressed.

k

integer. Length of counted DNA k-mers.

kIndex

integer. Numeric values which represent indices of DNA-k mers.

Value

. The length of the list equals the number of given filenames. Contains for each given file a matrix. Each matrix has one row for each given kIndex and an additional row with counts for all other DNA k-mers (labeled other). The number of columns equals the maximal sequence length in the FASTQ file.

Details

Maximal allowed value for k is 12.

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 1767-1771

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
k <- 4
kMers <- c("AAAA", "AACC", "AAGG")
kIdx <- kMerIndex(kMers)
res <- fastqKmerSubsetLocs("test_l6.fq", k, kIdx)