stringgaussnet (version 1.1)

getSTRINGNet: Get STRING network from gene identifiers

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

Value

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

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().

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)