SequencingSummaryReadLengthQualityDensity: plot a density map of sequence lengths and quality scores
In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Description
Usage
Arguments
Value
Examples
View source: R/SequencingSummary.R
Description
plots the density plot of read length against read mean quality scores
Usage
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SequencingSummaryReadLengthQualityDensity(seqsum=NA,
binFilter = 2,
qcThreshold = 7
)
Arguments
seqsum
is the data.frame object as prepared by importSequencingSummary
binFilter
is the minimum number of reads to include a cell in plot
(removes speckle)
qcThreshold
is the QC threshold used
Value
ggplot2 showing densities of read length and quality distribution
Examples
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init()
seqsumFile <- system.file("extdata",
"sequencing_summary.txt.bz2", package = "nanopoRe")
seqsum <- importSequencingSummary(seqsumFile)
plot <- SequencingSummaryReadLengthQualityDensity(seqsum)
sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.
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Description Usage Arguments Value Examples
View source: R/SequencingSummary.R
Description
plots the density plot of read length against read mean quality scores
Usage
1 2 3 4 | SequencingSummaryReadLengthQualityDensity(seqsum=NA,
binFilter = 2,
qcThreshold = 7
)
|
Arguments
seqsum |
is the data.frame object as prepared by importSequencingSummary |
binFilter |
is the minimum number of reads to include a cell in plot (removes speckle) |
qcThreshold |
is the QC threshold used |
Value
ggplot2 showing densities of read length and quality distribution
Examples
1 2 3 4 5 | init()
seqsumFile <- system.file("extdata",
"sequencing_summary.txt.bz2", package = "nanopoRe")
seqsum <- importSequencingSummary(seqsumFile)
plot <- SequencingSummaryReadLengthQualityDensity(seqsum)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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