Nonpareil.Curve-class: A single Nonpareil curve. This object can be produced by...
In Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'
Description
A single Nonpareil curve. This object can be produced by
Nonpareil.curve and supports S4 methods plot, summary,
print, and predict. For additional details, see help for
summary.Nonpareil.Curve.
Slots
fileInput .npo file.
labelName of the dataset.
colColor of the dataset.
LRead length.
ALAdjusted read length (same as L for alignment).
RNumber of reads.
LREffective sequencing effort used.
overlapMinimum read overlap.
ksizeK-mer size (for kmer kernel only).
log.sampleMultiplier of the log-sampling (or zero if linear).
kernelRead-comparison kernel.
versionNonpareil version used.
x.obsRarefied sequencing effort.
x.adjAdjusted rarefied sequencing effort.
y.redRarefied redundancy (observed).
y.covRarefied coverage (corrected).
y.sdStandard deviation of rarefied coverage.
y.p25Percentile 25 (1st quartile) of rarefied coverage.
y.p50Percentile 50 (median) of rarefied coverage.
y.p75Percentile 75 (3rd quartile) of rarefied coverage.
kappaDataset redundancy.
CDataset coverage.
consistentIs the data sufficient for accurate estimation?
starCoverage considered 'nearly complete'.
has.modelWas the model successfully estimated?
warningWarnings generated on consistency or model fitting.
LRstarProjected seq. effort for nearly complete coverage.
modelRPearson's R for the estimated model.
diversityDataset Nd index of sequence diversity.
modelFitted sigmoidal model.
callCall producing this object.
Nonpareil documentation built on Jan. 29, 2022, 1:08 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
A single Nonpareil curve. This object can be produced by
Nonpareil.curve and supports S4 methods plot, summary,
print, and predict. For additional details, see help for
summary.Nonpareil.Curve.
Slots
fileInput .npo file.
labelName of the dataset.
colColor of the dataset.
LRead length.
ALAdjusted read length (same as L for alignment).
RNumber of reads.
LREffective sequencing effort used.
overlapMinimum read overlap.
ksizeK-mer size (for kmer kernel only).
log.sampleMultiplier of the log-sampling (or zero if linear).
kernelRead-comparison kernel.
versionNonpareil version used.
x.obsRarefied sequencing effort.
x.adjAdjusted rarefied sequencing effort.
y.redRarefied redundancy (observed).
y.covRarefied coverage (corrected).
y.sdStandard deviation of rarefied coverage.
y.p25Percentile 25 (1st quartile) of rarefied coverage.
y.p50Percentile 50 (median) of rarefied coverage.
y.p75Percentile 75 (3rd quartile) of rarefied coverage.
kappaDataset redundancy.
CDataset coverage.
consistentIs the data sufficient for accurate estimation?
starCoverage considered 'nearly complete'.
has.modelWas the model successfully estimated?
warningWarnings generated on consistency or model fitting.
LRstarProjected seq. effort for nearly complete coverage.
modelRPearson's R for the estimated model.
diversityDataset Nd index of sequence diversity.
modelFitted sigmoidal model.
callCall producing this object.
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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