enve.TRIBS-class: Enveomics: TRIBS S4 Class

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

Enveomics: TRIBS S4 Class

Description

Enve-omics representation of "Transformed-space Resampling In Biased Sets (TRIBS)". This object represents sets of distances between objects, sampled nearly-uniformly at random in "distance space". Subsampling without selection is trivial, since both the distances space and the selection occur in the same transformed space. However, it's useful to compare randomly subsampled sets against a selected set of objects. This is intended to identify overdispersion or overclustering (see enve.TRIBStest) of a subset against the entire collection of objects with minimum impact of sampling biases. This object can be produced by enve.tribs and supports S4 methods plot and summary.

Slots

distance

(numeric) Centrality measurement of the distances between the selected objects (without subsampling).

points

(matrix) Position of the different objects in distance space.

distances

(matrix) Subsampled distances, where the rows are replicates and the columns are subsampling levels.

spaceSize

(numeric) Number of objects.

selSize

(numeric) Number of selected objects.

dimensions

(numeric) Number of dimensions in the distance space.

subsamples

(numeric) Subsampling levels (as fractions, from 0 to 1).

call

(call) Call producing this object.

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 13, 2022, 5:10 p.m.