ogr2tni: Integrates evolutionary rooting information and regulatory...

In geneplast: Evolutionary and plasticity analysis of orthologous groups

Description

This function adds evolutionary rooting information to regulons of a TNI class object.

Usage

ogr2tni(ogr, cogdata, tni)

Arguments

ogr	a processed object of class 'OGR' evaluated by the groot method.
cogdata	a data.frame with COG to protein mapping, with at least one gene annotation type listed in the 'rtni' object (e.g. ENTREZ gene ID).
tni	a processed object of class 'TNI' TNI-class evaluated by the methods tni.permutation, tni.bootstrap and tni.dpi.filter.

Value

Return an updated TNI object with evolutionary root information.

Author(s)

Rodrigo Dalmolin, Mauro Castro, Sheyla Trefflich

References

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

See Also

OGR-class

Examples

## Not run: 
#This example requires the geneplast.data.string.v91 package! (currently available under request)

# Evolutionary rooting inference for all human genes

library(geneplast.data.string.v91)
data(gpdata_string_v91)

cogids <- cogdata$cog_id[cogdata$ssp_id=="9606"]
ogr <- groot.preprocess(cogdata=cogdata, phyloTree=phyloTree, spid="9606", cogids=cogids)

ogr <- groot(ogr, nPermutations=100, verbose=TRUE)

# Integrates evolutionary rooting information and regulons

library(RTN)
library(Fletcher2013b)
data("rtni1st")
rtni1st <- ogr2tni(ogr, cogdata, rtni1st)



## End(Not run)

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