mpress-class: An S4 class representing the MPrESS data and output

In JCVenterInstitute/MPress: Microbiome Power Estimation with Sampling and Simulation

An S4 class representing the MPrESS data and output

Description

An S4 class representing the MPrESS data and output

Slots

dist.mst

The distance matrix showing the distances between different genomes

phy

The phylogenetic tree in newick format

rank

The ranks of the respective genomes with lower getting higher priority in being called as a medoid

cluster

A vector giving the numeric cluster ID for each genome

h

The threshold variable used to make the clusters

medoids

A vector giving the medoid for each cluster

gmm

A data.frame containing all the gaussian distributions used to find the threshold when available

gmm.orig

A data.frame containing all the gaussian distributions prior to cleaning. Used to recalculate the threshold when needed

annotation

A data.frame containing the annotations foreach genome with the genomes as the rows and the annotations with the columns. The

JCVenterInstitute/MPress documentation built on Jan. 1, 2023, 11:55 a.m.