groot.preprocess {geneplast} | R Documentation

## Evolutionary rooting inference.

### Description

Constructor for the 'OGR-class' object.

### Usage

    groot.preprocess(cogdata, phyloTree, spid, cogids=NULL, verbose=TRUE)

### Arguments

`cogdata` | a data frame with COG's data.
`phyloTree` | an object of class "phylo".
`spid` | a single character or integer value specifying the reference species to be used in the rooting algorithm. This species should be listed in the 'phyloTree'.
`cogids` | an optional data frame with COG's annotation. Alternatively, it can be a character vector with COG IDs.
`verbose` | a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

### Details

This function creates an `OGR-class` object and checks the consistency of the input data for the evolutionary root pipeline. Internally, the function access the presence and absence of orthologs for each species in a given OG and computes the `orthoct` data.frame.

### Value

A preprocessed object of class 'OGR'.

### Author(s)

Rodrigo Dalmolin, Mauro Castro

### References

Dalmolin RJ and Castro, MA. Geneplast: Evolutionary rooting using orthologous groups distribution. Journal Paper (in preparation), 2016.

### See Also

`OGR-class`

### Examples

    #load datasets used for demonstration
    data(gpdata.gs)

    #create and object of class 'OGR' for H. sapiens
    ogr <- groot.preprocess(cogdata=cogdata, phyloTree=phyloTree, spid="9606", cogids=cogids)

[Package geneplast version 1.6.2 Index]