getSeqlen-methods {qrqc} | R Documentation |
SequenceSummary
objectAn 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.
getSeqlen(x)
x |
an S4 object that inherits from |
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()