groot.preprocess: Evolutionary rooting inference.

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

View source: R/AllContructors.R

Description

Constructor for the 'OGR-class' object.

Usage

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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

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#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)

geneplast documentation built on Nov. 1, 2018, 2:27 a.m.