Nonpareil.Curve-class: A single Nonpareil curve. This object can be produced by...

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

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.

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

file

Input .npo file.

label

Name of the dataset.

col

Color of the dataset.

L

Read length.

AL

Adjusted read length (same as L for alignment).

R

Number of reads.

LR

Effective sequencing effort used.

overlap

Minimum read overlap.

ksize

K-mer size (for kmer kernel only).

log.sample

Multiplier of the log-sampling (or zero if linear).

kernel

Read-comparison kernel.

version

Nonpareil version used.

x.obs

Rarefied sequencing effort.

x.adj

Adjusted rarefied sequencing effort.

y.red

Rarefied redundancy (observed).

y.cov

Rarefied coverage (corrected).

y.sd

Standard deviation of rarefied coverage.

y.p25

Percentile 25 (1st quartile) of rarefied coverage.

y.p50

Percentile 50 (median) of rarefied coverage.

y.p75

Percentile 75 (3rd quartile) of rarefied coverage.

kappa

Dataset redundancy.

C

Dataset coverage.

consistent

Is the data sufficient for accurate estimation?

star

Coverage considered 'nearly complete'.

has.model

Was the model successfully estimated?

warning

Warnings generated on consistency or model fitting.

LRstar

Projected seq. effort for nearly complete coverage.

modelR

Pearson's R for the estimated model.

diversity

Dataset Nd index of sequence diversity.

model

Fitted sigmoidal model.

call

Call producing this object.

Nonpareil documentation built on June 28, 2024, 5:09 p.m.