HTSanalyzeR (version 2.24.0)

interactome: Create an interactome from BioGRID data sets

Description

This is a generic function.

When implemented as the S4 method of class NWA, this function creates an interactome before conducting network analysis.

To use this function for objects of class NWA:

interactome(object, interactionMatrix, species, link, reportDir = "HTSanalyzerReport", genetic=FALSE, verbose=TRUE)

Usage

interactome(object, ...)

Arguments

object

an object. When this function is implemented as the S4 method of class NWA, this argument is an object of class 'NWA'

...

other arguments (see below for the arguments supported by the method of class NWA)

Value

In the end, this function will return an updated object with slot 'interactome' as an object of class graphNEL.

Details

This function provides two options to create an interactome for network analysis. The user can either input an interaction matrix including columns 'InteractionType', 'InteractionA' and 'InteractionB', or set 'species', 'link' and 'genetic' to download data set from BioGRID and extract corresponding interactions to build the interactome.

Another way to set up the interactome is to input a graphNEL object when the NWA object is created (i.e. nwa=new("NWA", pvalues, phenotypes, interactome)).

See Also

biogridDataDownload, NWA

Examples

## Not run: 
# ##example 1, input interactome when initializing an 'NWA' object
# ##load p-values and phenotypes
# data("KcViab_PVals","KcViab_Data4Enrich")
# ##load BioGRID interactome for Drosophila Melanogaster
# data("Biogrid_DM_Interactome")
# ##create a NWA (NetWork Analysis) object
# nwa <- new("NWA",pvalues=KcViab_PVals, phenotypes=KcViab_Data4Enrich, 
# interactome=Biogrid_DM_Interactome)
# ##print nwa
# nwa
# 
# library(BioNet)
# ##example 2, build an interactome from Biogrid data base
# ##create a NWA (NetWork Analysis) object
# nwa <- new("NWA", pvalues=KcViab_PVals, phenotypes=KcViab_Data4Enrich)
# ##print nwa
# nwa
# ##download data from BioGRID and build the interactome
# nwa <- interactome(nwa, species="Dm", reportDir="NWATest")
# ##print nwa again
# nwa
# ## End(Not run)