Plot Entropy of k-mers by Position

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Description

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.

Usage

1

Arguments

x

an S4 object a class that inherits from SequenceSummary from readSeqFile or a list of objects that inherit from SequenceSummary with names.

Methods

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.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

getKmer, calcKL, kmerKLPlot

Examples

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  ## 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))

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