getBase-methods {qrqc} | R Documentation |
SequenceSummary
ObjectAn object that inherits from class SequenceSummary
contains
base frequency data by position gathered by readSeqFile
. getBase
is an accessor function that reshapes the base frequency data by position
into a data frame.
This accessor function is useful if you want to map variables to
custom ggplot2
aesthetics. Base proportions can be accessed
with getBaseProp
.
getBase(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. |
getBase
returns a data.frame
with columns:
position |
the position in the read. |
base |
the base. |
frequency |
the number of a base found per position in the read. |
signature(x = "SequenceSummary")
getBase
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
, getBaseProp
, 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(getBase(s.fastq)) + geom_line(aes(x=position, y=frequency, color=base)) + facet_grid(. ~ base) + scale_color_dna()