getGC-methods: Get a Data Frame of GC Content from a 'SequenceSummary'...
In qrqc: Quick Read Quality Control

Description Usage Arguments Value Methods Author(s) See Also Examples

An object that inherits from class SequenceSummary contains base frequency data by position gathered by readSeqFile. getGC is an accessor function that reshapes the base frequency data into a data frame and returns the GC content by position.

This accessor function is useful if you want to map variables to custom ggplot2 aesthetics. Frequencies or proportions of all bases (not just GC) can be accessed with getBase and getBaseProp respectively.

  getGC(x)

`x`	an S4 object that inherits from `SequenceSummary` from `readSeqFile`.

getGC returns a data.frame with columns:

`position`	the position in the read.
`gc`	GC content per position in the read.

signature(x = "SequenceSummary"): getGC is an accessor function that works on any object read in with readSeqFile; that is, objects that inherit from SequenceSummary.

Vince Buffalo <vsbuffalo@ucdavis.edu>

getSeqlen, getBase, getBaseProp, getQual, getMCQual, getKmer, gcPlot

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

  # A custom GC plot
  d <- merge(getQual(s.fastq), getGC(s.fastq), by.x="position", by.y="position")
  p <- ggplot(d) + geom_linerange(aes(x=position, ymin=lower,
    ymax=upper, color=gc)) + scale_color_gradient(low="red",
    high="blue") + scale_y_continuous("GC content")
  p