groot.preprocess: Evolutionary rooting inference.
In geneplast: Evolutionary and plasticity analysis of orthologous groups

Description Usage Arguments Details Value Author(s) References See Also Examples

Constructor for the 'OGR-class' object.

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

`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).

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.

A preprocessed object of class 'OGR'.

Rodrigo Dalmolin, Mauro Castro

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

OGR-class

#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)