kmerEntropyPlot-methods {qrqc} | R Documentation |
kmerEntropyPlot
plots the Shannon entropy per position of
k-mers. Lower Shannon entropy implies that the distribution of k-mers
is non-random and could indicate bias.
kmerEntropyPlot(x)
x |
an S4 object a class that inherits from |
signature(x = "SequenceSummary")
kmerEntropyPlot
will plot Shannon entropy per position for an
object that inherits from SequenceSummary
.
signature(x = "list")
kmerEntropyPlot
will plot the Shannon entropy per position
for each of the objects that inherit from SequenceSummary
in
the list and display them in a series of panels.
Vince Buffalo <vsbuffalo@ucdavis.edu>
## Load a somewhat contaminated FASTQ file s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'), hash.prop=1) ## Load a really contaminated FASTQ file s.contam.fastq <- readSeqFile(system.file('extdata', 'test-contam.fastq', package='qrqc'), hash.prop=1) ## Load a random (equal base frequency) FASTA file s.random.fasta <- readSeqFile(system.file('extdata', 'random.fasta', package='qrqc'), type="fasta", hash.prop=1) ## Plot the Shannon entropy for a single file kmerEntropyPlot(s.fastq) ## Plot the Shannon entropy for many files kmerEntropyPlot(list("highly contaminated"=s.contam.fastq, "less contaminated"=s.fastq, "random"=s.random.fasta))