enve.RecPlot2.Peak-class: Enveomics: Recruitment Plot (2) Peak - S4 Class

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Recruitment Plot (2) Peak - S4 Class

Description

Enve-omics representation of a peak in the sequencing depth histogram of a Recruitment plot (see enve.recplot2.findPeaks).

Slots

dist

(character) Distribution of the peak. Currently supported: norm (normal) and sn (skew-normal).

values

(numeric) Sequencing depth values predicted to conform the peak.

values.res

(numeric) Sequencing depth values not explained by this or previously identified peaks.

mode

(numeric) Seed-value of mode anchoring the peak.

param.hat

(list) Parameters of the distribution. A list of two values if dist=norm (sd and mean), or three values if dist=sn(omega=scale, alpha=shape, and xi=location). Note that the "dispersion" parameter is always first and the "location" parameter is always last.

n.hat

(numeric) Number of bins estimated to be explained by this peak. This should ideally be equal to the length of values, but it's not an integer.

n.total

(numeric) Total number of bins from which the peak was extracted. I.e., total number of position bins with non-zero sequencing depth in the recruitment plot (regardless of peak count).

err.res

(numeric) Error left after adding the peak (mower) or log-likelihood (em or emauto).

merge.logdist

(numeric) Attempted merge.logdist parameter.

seq.depth

(numeric) Best estimate available for the sequencing depth of the peak (centrality).

log

(logical) Indicates if the estimation was performed in natural logarithm space.

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 3, 2025, 9:06 p.m.