getSTRINGNet: Get STRING network from gene identifiers

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

Description

This function gets PPIs interactions between given genes through the STRING API. This functions uses an URI to query STRING, then an internet connection is required.

Usage

getSTRINGNet(DEGeneExpr, Identifier = 0, NAdditionalNodes = NA, Species = 9606,
	ConvertAliases = T, AddAnnotations = F, MartDataset = "hsapiens_gene_ensembl")

Arguments

DEGeneExpr	Object of class DEGeneExpr. See DEGeneExpr.default() for more details.
Identifier	Which column in DE genes analysis results DEGeneExpr object is used as identifier for STRING. By default row names are taken when it equals to 0.
NAdditionalNodes	Number of additional nodes inserted by STRING
Species	From which species come gene identifiers. By default it is homo sapiens (9606).
ConvertAliases	Boolean variable indicating whether gene symbol aliases must be converted to HGNC symbols.
AddAnnotations	Boolean variable indicating whether gene annotations must be added through biomaRt
MartDataset	Which mart dataset to use for querying gene annotations through biomaRt

Details

Gene identifiers can be Ensembl IDs or HGNC symbols. STRING gives the number of additional nodes + 10 added nodes by default. If you don't want any additional nodes at all, you can set NAdditionalNodes = NULL. By default, when NAdditionalNodes is NA, twice the number of initial nodes + 10 are added. Species are entered with taxon identifiers. To see correspondance, please have a look here: http://www.uniprot.org/taxonomy Aliases are converted with the package limma. No internet connection is needed for this step. 2 kinds of annotations are added. First, stringgaussnet uses the R package biomart to get mainly genomic localization and gene description. Secondly, it adds cellular component terms with the package AnnotationDbi. A prioritization is performed to rank gene products localizations from nuclear, the most relevant, and then extracellular, plasma membrane and cytoplasm. To know which mart dataset to use for given species, please use getMartDatasets().

Value

An object of class STRINGNet. See STRINGNet.default() for more details.

See Also

print.STRINGNet, summary.STRINGNet, export.STRINGNet, getShortestPaths, getMartDatasets, selectInteractionTypes

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.