Fastq objectsGeneric functions for plotting and printing the content of a Fastq object.
# S3 method for Fastq
plot(x, y = NULL, col = "tan4", border = "tan4", ...)# S3 method for Fastq
summary(object, ...)
A Fastq object, see below.
not used.
Color of bar interiors.
Color of bar borders.
Optional graphical arguments.
A Fastq object, see below.
A Fastq object contains biological sequences in the FASTQ format. It is a small (S3)
extension to a data.frame. It is actually a data.frame containing at least three text columns
named Header, Sequence and Quality. The Header column contains the headerlines
for each sequence, the Sequence columns the sequences themselves and the Quality the base-quality
sequence. A Fastq object is typically created by reading
a FASTQ formatted file into R by readFastq.
A Fastq object can be treated as a data.frame, which makes it quick and easy to search both
for specific regular expressions, sort or re-arrange the ordering of the sequences,
extract subsets or add new data to an existing Fastq object.
A Fastq object can also be treated as a Fasta object. Using writeFasta
will write the Fastq to a file in Fasta format.
The plot.Fastq function will display the content of the Fastq object as a histogram over
the lengths of the sequences.
The summary.Fastq function will display a text giving the number of sequences and the alphabet,
i.e. listing all unique symbols found in the file.
# NOT RUN {
# See the examples in the Help-file for readFastq/writeFastq
# }
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