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)
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filenames |
Vector of fastq file names. Files can be gz compressed. |
k |
Length of counted DNA k-mers. |
probeLabel |
|
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
1 2 3 4 5 6 7 | 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"))
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