callBionet: Compute a maximum scoring subnetwork
In kwanjeeraw/metabox: metabox

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

compute a maximum scoring subnetwork from p-values of the nodes of a network. The function wraps around the main steps of BioNet including fitBumModel, scoreNodes, runFastHeinz to compute a subnetwork.

1	callBionet(edgelist, nodelist, pval, fdr)

`edgelist`	a data frame of edges contains at least a source column (1st column) and a target column (2nd column).
`nodelist`	a data frame of nodes contains node attributes e.g. node id, node name, node xref. Default is NULL.
`pval`	a numeric vector of p-values with name attributes identical to the names of network nodes.
`fdr`	a numeric value specifying false discovery rate. Default is 0.05.

list of data frame of nodes and data frame of edges with the following components:

nodes:

nodeAttributes = node attributes provided

score = node score: positive values = signal content and negative values = background noise

edges:

source, target

edgeAttributes = edge attributes provided

Return list of empty data frame if error or found nothing.

Kwanjeera W kwanich@ucdavis.edu

Beisser D., Klau GW., Dandekar T., Müller T. and Dittrich MT. (2010) BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics, 26(8):1129-30

Dittrich MT., Klau GW., Rosenwald A., Dandekar T., Müller T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24(13):i223-31

fitBumModel, scoreNodes, runFastHeinz

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#simnw <- computeSimilarity(c(1110,10413,196,51,311,43,764,790)) #compute similarity network for given pubchem compounds
#pval <- data.frame(pubchem=c(1110,10413,196,51,311,43,764,790),stat=runif(8, 0, 0.06)) #statistical values of pubchem compounds
#result <- computeSubnetwork(sim$edges,sim$nodes,pval=pval,internalid = F)

kwanjeeraw/metabox documentation built on May 20, 2019, 7:07 p.m.