seqTools (version 1.6.0)

fastqq: fastqq function: Reading summarizing information from FASTQ files.

Description

Reads read numbers, read lengths, counts per position alphabet frequencies, phred scores and counts per file DNA k-mers from (possibly compressed) FASTQ files.

Usage

fastqq(filenames, k=6, probeLabel)

Arguments

filenames

Vector of FASTQ file names. Files can be gz compressed.

k

Length of counted DNA k-mers.

probeLabel

character: Textual label for each probe. When probeLabel and filenames have different length, a warning is thrown and the given labels are discarded.

Value

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

See Also

Fastqq-class

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq <- fastqq("test_l6.fq")
fq <- fastqq("test_l6_multi_line.fq")
fq <- fastqq("non_exist.fq")
fq <- fastqq("test_l10_ATCGN.fq")
fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4,
                                                    probeLabel=c("g4", "g5"))