Description Usage Arguments Details Value Author(s) References See Also Examples
compute a subnetwork from p-values of the nodes of a network.
1 | computeSubnetwork(edgelist, nodelist, pval, fc, fdr, pcol, internalid, method, hasatt, returnas)
|
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 or a two-column data frame of statistical values e.g. p-values.
If |
fc |
a numeric vector of fold changes with name attributes identical to the names of network nodes. Default is NULL. |
fdr |
a numeric value specifying false discovery rate. Default is 0.05. |
pcol |
a string specifying columnname containing p-values. This parameter is only for accepting the input from GUI. |
internalid |
a logical value indicating whether the network nodes are neo4j ids, if TRUE (default). It has no effect if there is no database installed. |
method |
a string specifying the method used to compute the subnetwork. Default is bionet. |
hasatt |
a logical value indicating whether node attributes are kept already. Used by GUI. |
returnas |
a string specifying output type. It can be one of dataframe, list, json. Default is dataframe. |
For the method bionet
, the function wraps around the main steps of BioNet including fitBumModel
, scoreNodes
, runFastHeinz
to compute a subnetwork.
list of network information with the following components:
nodes:
nodeAttributes
= node attributes provided
score
= node score if the method is bionet
: positive values = signal content and negative values = background noise
edges:
source, target
edgeAttributes
= edge attributes provided
Return empty list 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
1 2 3 | #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(simnw$edges, simnw$nodes, pval=pval, internalid = F)
|
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