selectInteractionTypes: Select interaction sources in STRINGNet object

In stringgaussnet: PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

Description

This function allows to select specific interaction sources in an object of class STRINGNet, for example coexpression or experimental. This is also possible to filter on confidence score with this function.

Usage

selectInteractionTypes(Network, InteractionTypes = "All", Threshold = 0)

Arguments

Network	Object of class STRINGNet
InteractionTypes	Character vector indicating which interaction sources you are looking for. See details for possible values. If "All", no selection is made and only filtering on Threshold is processed.
Threshold	Numeric. Minimum threshold of confident score for selecting edges.

Details

Interaction sources can be coexpression, cooccurence, experimental, knowledge, neighborhood or textmining. Search for STRING DB help page to know what mean those interaction sources.

Value

A new object of class STRINGNet after edge filtering.

See Also

STRINGNet, STRINGNet.default, getSTRINGNet, print.STRINGNet, summary.STRINGNet, export.STRINGNet

Examples

data(SpADataExpression)
data(SpADEGenes)
SpAData<-DEGeneExpr(t(SpADataExpression),SpADEGenes)

# SpASTRINGNet<-getSTRINGNet(SpAData)
# Can be longer.

# SpASTRINGNet<-getSTRINGNet(SpAData,AddAnnotations=FALSE)
# print(SpASTRINGNet,5)
# summary(SpASTRINGNet)
# PPISpASTRINGNet<-selectInteractionTypes(SpASTRINGNet,
#	c("coexpression","experimental","knowledge"),0.9)

# shortPathSpANet<-getShortestPaths(PPISpASTRINGNet)
# shortPathSpANet<-FilterEdges(shortPathSpANet,2.2)
# print(shortPathSpANet,5)
# summary(shortPathSpANet)

stringgaussnet documentation built on May 29, 2017, 10:50 a.m.