Nonpareil (version 3.5.3)

Metagenome Coverage Estimation and Projections for 'Nonpareil'

Description

Plot, process, and analyze NPO files produced by 'Nonpareil' .

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Version

Install

install.packages('Nonpareil')

Monthly Downloads

268

Version

3.5.3

License

Artistic-2.0

Maintainer

Luis M RodriguezR

Last Published

June 28th, 2024

Functions in Nonpareil (3.5.3)

Nonpareil.antif

Complement function of Nonpareil.f.

Nonpareil.curve.batch

Alias of Nonpareil.set.

Nonpareil.read_data

Read the data tables and extract direct estimates.

Nonpareil.read_metadata

Read the metadata headers.

Nonpareil.f

Function of the projected model.

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.

Nonpareil.fit_model

Fit the sigmoidal model to the rarefied coverage.

Nonpareil.legend

Generates a legend for Nonpareil plots.

Nonpareil.coverage_factor

Factor to transform redundancy into coverage (internal function).

Nonpareil.curve

Generates a Nonpareil curve from an .npo file

$,Nonpareil.Set-method

Get attribute.

Nonpareil

Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'.

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.Set-class

Collection of Nonpareil.Curve objects. This object can be produced by Nonpareil.curve.batch and supports S4 methods plot, summary, and print.

Nonpareil.add.curve

Adds a Nonpareil.Curve to a Nonpareil.Set.

$<-,Nonpareil.Set-method

Set attribute.

Nonpareil.set

Generates a collection of Nonpareil curves (a Nonpareil.Set object) and (optionally) plots all of them in a single canvas.

$<-,Nonpareil.Curve-method

Set attribute.

plot.Nonpareil.Curve

Plot a Nonpareil.Curve object.

+,Nonpareil.Set,ANY-method

Alias of Nonpareil.add.curve.

predict.Nonpareil.Curve

Predict the coverage for a given sequencing effort.

$,Nonpareil.Curve-method

Get attribute.

plot.Nonpareil.Set

Plot a Nonpareil.Set object.

print.Nonpareil.Curve

Prints and returns invisibly a summary of the Nonpareil.Curve results.

summary.Nonpareil.Set

Returns a summary of the Nonpareil.Set results.

Nonpareil.col

Returns the color of the curve.