SequenceSummary
objectSequenceSummary
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)
SequenceSummary
from
readSeqFile
.getSeqlen
returns a data.frame
with columns:signature(x = "SequenceSummary")
getSeqlen
is an accessor function that works on any object read
in with readSeqFile
; that is, objects that inherit from
SequenceSummary
.
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()
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