getSeqlen-methods: Get a Data Frame of Sequence Lengths from a 'SequenceSummary'...
In qrqc: Quick Read Quality Control

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

An object that inherits from class SequenceSummary contains sequence length data by position gathered by readSeqFile. getSeqlen is an accessor function that returns the sequence length data.

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

1	getSeqlen(x)

`x`	an S4 object that inherits from `SequenceSummary` from `readSeqFile`.

getSeqlen returns a data.frame with columns:

`length`	the sequence length.
`count`	the number of reads with this sequence length.

signature(x = "SequenceSummary"): getSeqlen 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, getBase, getBaseProp, getQual, getMCQual, seqlenPlot

  library(ggplot2)

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

  # A custom plot - a bit contrived, but should show power
  d <- merge(getSeqlen(s.trimmed.fastq), getQual(s.trimmed.fastq),
    by.x="length", by.y="position")
  ggplot(d) + geom_linerange(aes(x=length, ymin=0, ymax=count),
    color="grey") + geom_linerange(aes(x=length, ymin=lower, ymax=upper),
    color="blue") + scale_y_continuous("quality/count") + theme_bw()