enve.RecPlot2.Peak-class: enve.RecPlot2.Peak S4 class

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

Description

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

Objects from the Class

Objects can be created by calls of the form new(enve.RecPlot2.Peak ...)

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 and 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.

merge.logdist:

(numeric) Attempted 'merge.logdist' parameter.

Methods

$

signature(x = "enve.RecPlot2.Peak"): ...

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on May 30, 2017, 5:19 a.m.