seqTools (version 1.6.0)

Fastqq-class: Class "Fastqq"

Description

Contains quality related summarizing data on FASTQ files.

Objects from the Class

Objects can be created by calls of the form fastqq("test.fq").

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

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq <- fastqq(c("g4_l101_n100.fq.gz","g5_l101_n100.fq.gz"), 
                                k=4, probeLabel=c("g4","g5"))
#
fileNames(fq)
getK(fq)
nNnucs(fq)
nFiles(fq)
nReads(fq)
maxSeqLen(fq)
collectTime(fq)
collectDur(fq)
slc<-seqLenCount(fq)
nf<-nucFreq(fq,1)
nf[1:4,1:10]
seqLen(fq)
probeLabel(fq)
probeLabel(fq) <- 1:nFiles(fq)
#
kc<-kmerCount(fq)
kc[1:10, ]
plotKmerCount(fq)
#
ph<-phred(fq, 1)
ph[25:35,1:15]
pq <- phredQuantiles(fq,c(0.25, 0.5, 0.75), 1)
plotNucFreq(fq, 1)
# Nucleotide count
plotNucCount(fq, 2:3) 
# GC content
gcContent(fq, 1)
#
fqq<-fq[1]