gplast.preprocess: Evolutionary plasticity inference.

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

View source: R/AllContructors.R

Description

Constructor for the 'OGP-class' object.

Usage

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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

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

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

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