Get a Data Frame of Quality Data from a FASTQSummary object

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Description

An object of class FASTQSummary contains quality data (binned by readSeqFile). getQual is an accessor function that reshapes the data into a data frame.

This accessor function is useful if you want to map variables to custom ggplot2 aesthetics.

Usage

1

Arguments

x

an S4 object of class FASTQSummary from readSeqFile.

Value

getQual returns a data.frame with columns:

position

the position in the read.

ymin

the minimum quality found per a position in the read.

alt.lower

the 10% quantile found per a position in the read.

lower

the 25% quartile found per a position in the read.

middle

the median found per a position in the read.

upper

the 75% quartile found per a position in the read.

alt.upper

the 90% quantile found per a position in the read.

ymax

the maximum quality found per a position in the read.

mean

the mean quality (calculated from the binned data by using a weighted mean function) per the position in the read.

Methods

signature(x="FASTQSummary")

getQual is an accessor function that only works if there is quality data, thus it only works with objects of class FASTQSummary.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

getGC, getSeqlen, getBase, getBaseProp, getMCQual, qualPlot

Examples

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

  ## Mean quality by position
  p <- ggplot(getQual(s.fastq)) + geom_line(aes(x=position, y=mean), color="blue")
  p <- p + scale_y_continuous(limits=c(0, 42))
  p

  ## A different type of quality plot
  p <- ggplot(getQual(s.fastq)) + geom_linerange(aes(x=position,
    ymin=lower, ymax=upper, color=mean))
  p <- p +  scale_color_gradient("mean quality", low="red", high="green")
  p + scale_y_continuous("quality")

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