fastqq {seqTools} | R Documentation |
Reads read numbers, read lengths, counts per position alphabet frequencies, phred scores and counts per file DNA k-mers from (possibly compressed) FASTQ files.
fastqq(filenames, k=6, probeLabel)
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
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"))