gcPlot-methods: Plot GC Content by Position

Description Usage Arguments Methods Author(s) See Also Examples

Description

gcPlot plots the GC content by position in the read.

Usage

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  gcPlot(x, color="red")

Arguments

x

an S4 object that inherits from SequenceSummary from readSeqFile.

color

the color to use for the GC content line.

Methods

signature(x = "FASTQSummary")

gcPlot will plot the GC content for a single object that inherits from SequenceSummary.

signature(x = "list")

gcPlot will plot the GC content for each of the SequenceSummary items in the list and display them in a series of panels.

Author(s)

Vince Buffalo <[email protected]>

See Also

getBase, getBaseProp

Examples

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  ## Load a FASTQ file, with sequence hashing.
  s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))

  ## Plot GC content
  gcPlot(s.fastq)

  ## Plot multiple GC content plots
  s.trimmed.fastq <- readSeqFile(system.file('extdata',
    'test-trimmed.fastq', package='qrqc'))
  gcPlot(list("not trimmed"=s.fastq, "trimmed"=s.trimmed.fastq))

  ## Graphical features can be added
  gcPlot(s.trimmed.fastq) + geom_hline(yintercept=0.5, color="purple")

qrqc documentation built on Nov. 1, 2018, 2:24 a.m.