ShortPathSTRINGNet.default: Function to create object of class ShortPathSTRINGNet

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

Description

This function is used by getShorthestPaths() to convert results from the computation of shortest paths from STRING network.

Usage

## Default S3 method:
ShortPathSTRINGNet(x, DEGenes, GenesAnnotations = NULL, ...)

Arguments

x	The non-formatted shortest paths STRING network obtained by getShortestPaths.
DEGenes	DE genes analysis results, which are used for primary node attributes.
GenesAnnotations	Gene annotations got by biomaRt if it was requested by getSTRINGNetwork(). Those will be used as secondary node attributes.
...	Additional parameters. Not used here.

Value

A list with at least two data frames: - Edge attributes, with distances, intermediate nodes separated by commas, and number of intermediate nodes. - Node attributes given by DE genes analysis results. A third data frame giving gene annotations can be added if it is not null when calling the function.

See Also

ShortPathSTRINGNet, getShortestPaths, print.ShortPathSTRINGNet, summary.ShortPathSTRINGNet, export.ShortPathSTRINGNet

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.