OGR-class: Class '"OGR"': an S4 class for rooting analysis.

In geneplast: Evolutionary and plasticity analysis of orthologous groups

Description

This S4 class includes methods to do inferential analysis of evolutionary roots in a given species tree.

Objects from the Class

Objects can be created by calls to the "groot.preprocess" constructor.

Slots

cogids:

Object of class "data.frame", a data frame with COG's data.

tree:

Object of class "phylo", a given species tree.

spbranches:

Object of class "data.frame", a data frame listing branches of a given species tree.

orthoroot:

Object of class "data.frame", a data.frame with results from the 'groot' function (see return values in the OGR methods).

orthoct:

Object of class "data.frame", a data.frame with results from the 'groot.preprocess' function (see return values in the OGR methods).

status:

Object of class "character", a character value specifying the status of the OGR object based on the available methods.

Methods

groot

signature(object = "OGR"): see groot

groot.get

signature(object = "OGR"): see groot.get

Author(s)

Rodrigo Dalmolin, Mauro Castro

See Also

groot.preprocess

geneplast documentation built on Nov. 8, 2020, 7:57 p.m.