# Evolutionary and plasticity analysis of orthologous groups

## Documentation for package ‘geneplast’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

geneplast-package | Geneplast: an R package for evolutionary rooting and plasticity inference based on orthologous groups distribution.
geneplast | Geneplast: an R package for evolutionary rooting and plasticity inference based on orthologous groups distribution.
gpdata.gs | A pre-processed dataset for the geneplast package.
gplast | Evolutionary plasticity inference.
gplast-method | Class '"OGP"': an S4 class for genetic plasticity analysis.
gplast.get | Get information from individual slots in an OGP object.
gplast.get-method | Class '"OGP"': an S4 class for genetic plasticity analysis.
gplast.preprocess | Evolutionary plasticity inference.
groot | Evolutionary rooting inference.
groot-method | Class '"OGR"': an S4 class for rooting analysis.
groot.get | Get information from individual slots in an OGR object.
groot.get-method | Class '"OGR"': an S4 class for rooting analysis.
groot.integration-method | Class '"OGR"': an S4 class for rooting analysis.
groot.plot | Plot the inferred evolutionary root of a given OG or the map of LCAs of a given species.
groot.preprocess | Evolutionary rooting inference.
OGP-class | Class '"OGP"': an S4 class for genetic plasticity analysis.
OGR-class | Class '"OGR"': an S4 class for rooting analysis.
ogr2igraph | Integrates evolutionary rooting information and graphs.
ogr2tni | Integrates evolutionary rooting information and regulatory networks.
ppi.gs | A pre-processed igraph object for the geneplast package.