getMCQual-methods {qrqc} | R Documentation |
FASTQSummary
objectAn 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.
getMCQual(x, n=100)
x |
an S4 object that inherits from |
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)