fastqq: fastqq function: Reading summarizing information from FASTQ...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	fastqq(filenames, k=6, probeLabel)

`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.

Maximal allowed value for k is 12.

S4 Object of class 'Fastqq'.

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

Fastqq-class

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"))

Loading required package: zlibbioc
[fastqq] File ( 1/1) 'test_l6.fq'	done.
[fastqq] File ( 1/1) 'test_l6_multi_line.fq'	done.
[fastqq] File ( 1/1) 'non_exist.fq'
[fastqq] Can not open file 'non_exist.fq'!
[fastqq] File ( 1/1) 'test_l10_ATCGN.fq'	done.
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz'	done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz'	done.