Metagenome Coverage Estimation and Projections for 'Nonpareil'

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Documentation for package ‘Nonpareil’ version 3.4.0

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Nonpareil-package Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'.
$-method Get attribute.
$-method Get attribute.
$<--method Set attribute.
$<--method Set attribute.
+-method Alias of 'Nonpareil.add.curve'.
Nonpareil Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'.
Nonpareil.add.curve Adds a 'Nonpareil.Curve' to a 'Nonpareil.Set'.
Nonpareil.antif Complement function of 'Nonpareil.f'.
Nonpareil.col Returns the color of the curve.
Nonpareil.coverage_factor Factor to transform redundancy into coverage (internal function).
Nonpareil.curve Generates a Nonpareil curve from an .npo file
Nonpareil.Curve-class 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'.
Nonpareil.curve.batch Alias of 'Nonpareil.set'.
Nonpareil.f Function of the projected model.
Nonpareil.fit_model Fit the sigmoidal model to the rarefied coverage.
Nonpareil.legend Generates a legend for Nonpareil plots.
Nonpareil.read_data Read the data tables and extract direct estimates.
Nonpareil.read_metadata Read the metadata headers.
Nonpareil.set Generates a collection of Nonpareil curves (a 'Nonpareil.Set' object) and (optionally) plots all of them in a single canvas.
Nonpareil.Set-class Collection of 'Nonpareil.Curve' objects. This object can be produced by 'Nonpareil.curve.batch' and supports S4 methods 'plot', 'summary', and 'print'.
plot.Nonpareil.Curve Plot a 'Nonpareil.Curve' object.
plot.Nonpareil.Set Plot a 'Nonpareil.Set' object.
predict.Nonpareil.Curve Predict the coverage for a given sequencing effort.
print.Nonpareil.Curve Prints and returns invisibly a summary of the 'Nonpareil.Curve' results.
print.Nonpareil.Set Prints and returns invisibly a summary of the 'Nonpareil.Set' results.
summary.Nonpareil.Curve Returns a summary of the 'Nonpareil.Curve' results.
summary.Nonpareil.Set Returns a summary of the 'Nonpareil.Set' results.