ogr2tni {geneplast} | R Documentation

## Integrates evolutionary rooting information and regulatory networks.

### 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)

[Package geneplast version 1.13.2 Index]