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

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on 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.

Details

Maximal allowed value for k is 12.

Value

S4 Object of class 'Fastqq'.

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 1767-1771

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"))

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.