gplast.preprocess {geneplast} | R Documentation

## Evolutionary plasticity inference.

### Description

Constructor for the 'OGP-class' object.

### Usage

    gplast.preprocess(cogdata, sspids=NULL, cogids=NULL, verbose=TRUE)

### Arguments

`cogdata` | a data frame or matrix with COG's data.
`sspids` | an optional data frame with species annotation. Alternatively, it can be a character vector with species IDs.
`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 `OGP-class` object and checks the consistency of the input data for the evolutionary plasticity pipeline. Internally, the function counts the number of orthologs for each species in a given OG and computes the `orthodist` matrix.

### Value

A preprocessed object of class 'OGP'.

### Author(s)

Rodrigo Dalmolin, Mauro Castro

### References

Dalmolin, RJ, Castro, MA, Rybarczyk-Filho JL, Souza LH, de Almeida RM, Moreira JC. Evolutionary plasticity determination by orthologous groups distribution. Biol Direct. 2011 May 17;6:22. DOI: 10.1186/1745-6150-6-22.

Castro MA, Dalmolin RJ, Moreira JC, Mombach JC, de Almeida RM. Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Res. 2008 Nov;36(19):6269-83. DOI: 10.1093/nar/gkn636.

### See Also

`OGP-class`

### Examples

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

    #create and object of class 'OGP'
    ogp <- gplast.preprocess(cogdata=cogdata, sspids=sspids, cogids=cogids)

[Package geneplast version 1.20.1 Index]