qrqc (version 1.26.0)

getBaseProp-methods: Get a Data Frame of Base Proportion Data from a SequenceSummary object

Description

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.

Usage

getBaseProp(x, drop=TRUE)

Arguments

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.

Value

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.

Methods

signature(x = "SequenceSummary")

getBaseProp is an accessor function that works on any object read in with readSeqFile; that is, objects that inherit from SequenceSummary.

See Also

getGC, getSeqlen, getBase, getQual, getMCQual, basePlot

Examples

  ## 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()