Plot a Base Quality Boxplot by Position

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Description

plotQuals plots quality statistics by position. Optionally, it adds a lowess curve through the qualities, which is fit with data randomly drawn from the distribution of qualities at each position. A histogram of the sequence length distribution is plotted above the quality plot when histogram is TRUE.

A legend is plotted on the bottom left if legend is TRUE (this location is used because this where the bases are likely to be of highest quality, and thus not overlap the legend). The grey lines indicate the range of the 10% and 90% quantiles, the orange lines indicate the range of the 25% and 75% quartiles, the blue point is the median, the green dash is the mean, and the purple line is the lowess curve if lowess is TRUE.

Usage

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  plotQuals(obj, ylim='relative', lowess=TRUE, histogram=TRUE, legend=TRUE)

Arguments

obj

an S4 object of class FASTQSummary from readSeqFile.

ylim

either ‘relative’ or ‘fixed’, which will scale the y axis to either the relative range (from the data) or absolute range of qualities.

lowess

a logical value indicating whether to fit a lowess curve through the quality plot.

histogram

a logical value indicating whether to add a histogram of the sequence length distribution above the quality plot.

legend

a logical value indicating whether a legend is to be included.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

qualPlot

Examples

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## Not run: 
  ## Load a FASTQ file, with sequence hashing.
  s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))

  ## Plot Qualities
  plotQuals(s.fastq)

## End(Not run)

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