| getBaseProp-methods {qrqc} | R Documentation |
SequenceSummary objectAn object that inherits from class SequenceSummary contains
base frequency data by position gathered by readSeqFile. getBaseProp
is an accessor function that reshapes the base frequency data by position
into a data frame and calculates the proportions of each base per position.
This accessor function is useful if you want to map variables to
custom ggplot2 aesthetics. Base frequency be accessed
with getBase.
getBaseProp(x, drop=TRUE)
x |
an S4 object that inherits from |
drop |
a logical value indicating whether to drop bases that don't have any counts. |
getBaseProp returns a data.frame with columns:
position |
the position in the read. |
base |
the base. |
proportion |
the proportion of a base found per position in the read. |
signature(x = "SequenceSummary")getBaseProp 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, getSeqlen, getBase, getQual, getMCQual, basePlot
## Load a FASTQ file, with sequence hashing.
s.fastq <- readSeqFile(system.file('extdata', 'test.fastq',
package='qrqc'))
# A custom base plot
ggplot(getBaseProp(s.fastq)) + geom_line(aes(x=position, y=proportion,
color=base)) + facet_grid(. ~ base) + scale_color_dna()