getBaseProp-methods: Get a Data Frame of Base Proportion Data from a...
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. getBaseProp is an accessor function that reshapes the base frequency data by position into a data frame and calculates the proportions of each base per position.

This accessor function is useful if you want to map variables to custom ggplot2 aesthetics. Base frequency be accessed with getBase.

1	getBaseProp(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.

getBaseProp returns a data.frame with columns:

`position`	the position in the read.
`base`	the base.
`proportion`	the proportion of a base found per position in the read.

signature(x = "SequenceSummary"): getBaseProp 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, getBase, 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(getBaseProp(s.fastq)) + geom_line(aes(x=position, y=proportion,
    color=base)) + facet_grid(. ~ base) + scale_color_dna()