getMCQual-methods: Get a Data Frame of Simulated Qualitied from a 'FASTQSummary'...
In qrqc: Quick Read Quality Control

Description Usage Arguments Value Methods Author(s) See Also Examples

An object that inherits from class FASTQSummary contains base quality data by position gathered by readSeqFile. getMCQual generates simulated quality data for each base from this binned quality data that can be used for adding smoothed lines via lowess.

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

1	getMCQual(x, n=100)

`x`	an S4 object that inherits from `FASTQSummary` from `readSeqFile`.
`n`	a numeric value indicating the number of quality values to draw per base.

getMCQual returns a data.frame with columns:

`position`	the position in the read.
`quality`	simulated quality scores.

signature(x = "FASTQSummary"): getMCQual is a function that works on any object with class FASTQSummary read in with readSeqFile.

Vince Buffalo <vsbuffalo@ucdavis.edu>

getGC, getSeqlen, getBase, getBaseProp, getQual, qualPlot

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

  # A custom quality plot
  ggplot(getQual(s.fastq)) + geom_linerange(aes(x=position, ymin=lower,
    ymax=upper), color="grey") + geom_smooth(aes(x=position, y=quality),
    data=getMCQual(s.fastq), color="blue", se=FALSE)