getQual-methods {qrqc} | R Documentation |
FASTQSummary
objectAn 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.
getQual(x)
x |
an S4 object of class |
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. |
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
.
Vince Buffalo <vsbuffalo@ucdavis.edu>
getGC
, getSeqlen
,
getBase
, getBaseProp
,
getMCQual
, qualPlot
## 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")