getBase-methods: Get a Data Frame of Base Frequency Data from a...
In vsbuffalo/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. getBase is an accessor function that reshapes the base frequency data by position into a data frame.

This accessor function is useful if you want to map variables to custom ggplot2 aesthetics. Base proportions can be accessed with getBaseProp.

1	getBase(x, drop=TRUE)

`x`	an S4 object that inherits from `SequenceSummary` from `readSeqFile`.
`drop`	a logical value indicating whether to drop bases that don't have any counts.

getBase returns a data.frame with columns:

`position`	the position in the read.
`base`	the base.
`frequency`	the number of a base found per position in the read.

signature(x = "SequenceSummary"): getBase 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>

getGC, getSeqlen, getBaseProp, getQual, getMCQual, basePlot

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

  # A custom base plot
  ggplot(getBase(s.fastq)) + geom_line(aes(x=position, y=frequency,
    color=base)) + facet_grid(. ~ base) + scale_color_dna()